Mercurial > repos > glogobyte > mirviz
changeset 4:216888953a0a draft
Deleted selected files
| author | glogobyte |
|---|---|
| date | Wed, 13 Oct 2021 11:19:00 +0000 |
| parents | 64a48e3412f2 |
| children | 4d59ac081282 |
| files | README.md |
| diffstat | 1 files changed, 0 insertions(+), 1572 deletions(-) [+] |
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data-view-component="true" class="octicon octicon-repo js-jump-to-octicon-repo d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M2 2.5A2.5 2.5 0 014.5 0h8.75a.75.75 0 01.75.75v12.5a.75.75 0 01-.75.75h-2.5a.75.75 0 110-1.5h1.75v-2h-8a1 1 0 00-.714 1.7.75.75 0 01-1.072 1.05A2.495 2.495 0 012 11.5v-9zm10.5-1V9h-8c-.356 0-.694.074-1 .208V2.5a1 1 0 011-1h8zM5 12.25v3.25a.25.25 0 00.4.2l1.45-1.087a.25.25 0 01.3 0L8.6 15.7a.25.25 0 00.4-.2v-3.25a.25.25 0 00-.25-.25h-3.5a.25.25 0 00-.25.25z"></path> -</svg> - <svg title="Project" aria-label="Project" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project js-jump-to-octicon-project d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M1.75 0A1.75 1.75 0 000 1.75v12.5C0 15.216.784 16 1.75 16h12.5A1.75 1.75 0 0016 14.25V1.75A1.75 1.75 0 0014.25 0H1.75zM1.5 1.75a.25.25 0 01.25-.25h12.5a.25.25 0 01.25.25v12.5a.25.25 0 01-.25.25H1.75a.25.25 0 01-.25-.25V1.75zM11.75 3a.75.75 0 00-.75.75v7.5a.75.75 0 001.5 0v-7.5a.75.75 0 00-.75-.75zm-8.25.75a.75.75 0 011.5 0v5.5a.75.75 0 01-1.5 0v-5.5zM8 3a.75.75 0 00-.75.75v3.5a.75.75 0 001.5 0v-3.5A.75.75 0 008 3z"></path> -</svg> - <svg title="Search" aria-label="Search" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search js-jump-to-octicon-search d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path> -</svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - -</ul> - -<ul class="d-none js-jump-to-no-results-template-container"> - <li class="d-flex flex-justify-center flex-items-center f5 d-none js-jump-to-suggestion p-2"> - <span class="color-text-secondary">No suggested jump to results</span> - </li> -</ul> - -<ul id="jump-to-results" role="listbox" class="p-0 m-0 js-navigation-container jump-to-suggestions-results-container js-jump-to-suggestions-results-container"> - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-scoped-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="" data-item-type="scoped_search"> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg title="Repository" aria-label="Repository" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo js-jump-to-octicon-repo d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M2 2.5A2.5 2.5 0 014.5 0h8.75a.75.75 0 01.75.75v12.5a.75.75 0 01-.75.75h-2.5a.75.75 0 110-1.5h1.75v-2h-8a1 1 0 00-.714 1.7.75.75 0 01-1.072 1.05A2.495 2.495 0 012 11.5v-9zm10.5-1V9h-8c-.356 0-.694.074-1 .208V2.5a1 1 0 011-1h8zM5 12.25v3.25a.25.25 0 00.4.2l1.45-1.087a.25.25 0 01.3 0L8.6 15.7a.25.25 0 00.4-.2v-3.25a.25.25 0 00-.25-.25h-3.5a.25.25 0 00-.25.25z"></path> -</svg> - <svg title="Project" aria-label="Project" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project js-jump-to-octicon-project d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M1.75 0A1.75 1.75 0 000 1.75v12.5C0 15.216.784 16 1.75 16h12.5A1.75 1.75 0 0016 14.25V1.75A1.75 1.75 0 0014.25 0H1.75zM1.5 1.75a.25.25 0 01.25-.25h12.5a.25.25 0 01.25.25v12.5a.25.25 0 01-.25.25H1.75a.25.25 0 01-.25-.25V1.75zM11.75 3a.75.75 0 00-.75.75v7.5a.75.75 0 001.5 0v-7.5a.75.75 0 00-.75-.75zm-8.25.75a.75.75 0 011.5 0v5.5a.75.75 0 01-1.5 0v-5.5zM8 3a.75.75 0 00-.75.75v3.5a.75.75 0 001.5 0v-3.5A.75.75 0 008 3z"></path> -</svg> - <svg title="Search" aria-label="Search" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search js-jump-to-octicon-search d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path> -</svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-owner-scoped-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="" data-item-type="owner_scoped_search"> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg title="Repository" aria-label="Repository" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo js-jump-to-octicon-repo d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M2 2.5A2.5 2.5 0 014.5 0h8.75a.75.75 0 01.75.75v12.5a.75.75 0 01-.75.75h-2.5a.75.75 0 110-1.5h1.75v-2h-8a1 1 0 00-.714 1.7.75.75 0 01-1.072 1.05A2.495 2.495 0 012 11.5v-9zm10.5-1V9h-8c-.356 0-.694.074-1 .208V2.5a1 1 0 011-1h8zM5 12.25v3.25a.25.25 0 00.4.2l1.45-1.087a.25.25 0 01.3 0L8.6 15.7a.25.25 0 00.4-.2v-3.25a.25.25 0 00-.25-.25h-3.5a.25.25 0 00-.25.25z"></path> -</svg> - <svg title="Project" aria-label="Project" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project js-jump-to-octicon-project d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M1.75 0A1.75 1.75 0 000 1.75v12.5C0 15.216.784 16 1.75 16h12.5A1.75 1.75 0 0016 14.25V1.75A1.75 1.75 0 0014.25 0H1.75zM1.5 1.75a.25.25 0 01.25-.25h12.5a.25.25 0 01.25.25v12.5a.25.25 0 01-.25.25H1.75a.25.25 0 01-.25-.25V1.75zM11.75 3a.75.75 0 00-.75.75v7.5a.75.75 0 001.5 0v-7.5a.75.75 0 00-.75-.75zm-8.25.75a.75.75 0 011.5 0v5.5a.75.75 0 01-1.5 0v-5.5zM8 3a.75.75 0 00-.75.75v3.5a.75.75 0 001.5 0v-3.5A.75.75 0 008 3z"></path> -</svg> - <svg title="Search" aria-label="Search" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search js-jump-to-octicon-search d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path> -</svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this user"> - In this user - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - - -<li class="d-flex flex-justify-start flex-items-center p-0 f5 navigation-item js-navigation-item js-jump-to-global-search d-none" role="option"> - <a tabindex="-1" class="no-underline d-flex flex-auto flex-items-center jump-to-suggestions-path js-jump-to-suggestion-path js-navigation-open p-2" href="" data-item-type="global_search"> - <div class="jump-to-octicon js-jump-to-octicon flex-shrink-0 mr-2 text-center d-none"> - <svg title="Repository" aria-label="Repository" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo js-jump-to-octicon-repo d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M2 2.5A2.5 2.5 0 014.5 0h8.75a.75.75 0 01.75.75v12.5a.75.75 0 01-.75.75h-2.5a.75.75 0 110-1.5h1.75v-2h-8a1 1 0 00-.714 1.7.75.75 0 01-1.072 1.05A2.495 2.495 0 012 11.5v-9zm10.5-1V9h-8c-.356 0-.694.074-1 .208V2.5a1 1 0 011-1h8zM5 12.25v3.25a.25.25 0 00.4.2l1.45-1.087a.25.25 0 01.3 0L8.6 15.7a.25.25 0 00.4-.2v-3.25a.25.25 0 00-.25-.25h-3.5a.25.25 0 00-.25.25z"></path> -</svg> - <svg title="Project" aria-label="Project" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project js-jump-to-octicon-project d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M1.75 0A1.75 1.75 0 000 1.75v12.5C0 15.216.784 16 1.75 16h12.5A1.75 1.75 0 0016 14.25V1.75A1.75 1.75 0 0014.25 0H1.75zM1.5 1.75a.25.25 0 01.25-.25h12.5a.25.25 0 01.25.25v12.5a.25.25 0 01-.25.25H1.75a.25.25 0 01-.25-.25V1.75zM11.75 3a.75.75 0 00-.75.75v7.5a.75.75 0 001.5 0v-7.5a.75.75 0 00-.75-.75zm-8.25.75a.75.75 0 011.5 0v5.5a.75.75 0 01-1.5 0v-5.5zM8 3a.75.75 0 00-.75.75v3.5a.75.75 0 001.5 0v-3.5A.75.75 0 008 3z"></path> -</svg> - <svg title="Search" aria-label="Search" role="img" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search js-jump-to-octicon-search d-none flex-shrink-0"> - <path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path> -</svg> - </div> - - <img class="avatar mr-2 flex-shrink-0 js-jump-to-suggestion-avatar d-none" alt="" aria-label="Team" src="" width="28" height="28"> - - <div class="jump-to-suggestion-name js-jump-to-suggestion-name flex-auto overflow-hidden text-left no-wrap css-truncate css-truncate-target"> - </div> - - <div class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none js-jump-to-badge-search"> - <span class="js-jump-to-badge-search-text-default d-none" aria-label="in this repository"> - In this repository - </span> - <span class="js-jump-to-badge-search-text-global d-none" aria-label="in all of GitHub"> - All GitHub - </span> - <span aria-hidden="true" class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - - <div aria-hidden="true" class="border rounded-1 flex-shrink-0 color-bg-tertiary px-1 color-text-tertiary ml-1 f6 d-none d-on-nav-focus js-jump-to-badge-jump"> - Jump to - <span class="d-inline-block ml-1 v-align-middle">↵</span> - </div> - </a> -</li> - - -</ul> - - </div> - </label> -</form> </div> -</div> - - </div> - - <div class="position-relative mr-3 mb-4 mb-lg-0 d-inline-block"> - <a href="/login?return_to=https%3A%2F%2Fgithub.com%2FGlogobyte%2FisomiR_tools%2Fblob%2Fmain%2FREADME.md" - class="HeaderMenu-link flex-shrink-0 no-underline" - data-hydro-click="{"event_type":"authentication.click","payload":{"location_in_page":"site header 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data-hydro-click="{"event_type":"analytics.event","payload":{"category":"Sign up","action":"click to sign up for account","label":"ref_page:/<user-name>/<repo-name>/blob/show;ref_cta:Sign up;ref_loc:header logged out","originating_url":"https://github.com/Glogobyte/isomiR_tools/blob/main/README.md","user_id":null}}" data-hydro-click-hmac="10b5589e3d935965ad52ca5d4bf93859e37d170f4f71e7efd5ec52c09a6e8b19" - > - Sign up - </a> - </div> - </div> - </div> -</header> - - </div> - - <div id="start-of-content" class="show-on-focus"></div> - - - - - - - <div data-pjax-replace id="js-flash-container"> - - - <template class="js-flash-template"> - <div class="flash flash-full {{ className }}"> - <div class=" px-2" > - <button class="flash-close js-flash-close" type="button" aria-label="Dismiss this message"> - <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> - <path fill-rule="evenodd" d="M3.72 3.72a.75.75 0 011.06 0L8 6.94l3.22-3.22a.75.75 0 111.06 1.06L9.06 8l3.22 3.22a.75.75 0 11-1.06 1.06L8 9.06l-3.22 3.22a.75.75 0 01-1.06-1.06L6.94 8 3.72 4.78a.75.75 0 010-1.06z"></path> -</svg> - </button> - - <div>{{ message }}</div> - - </div> -</div> - </template> -</div> - - - - - <include-fragment class="js-notification-shelf-include-fragment" data-base-src="https://github.com/notifications/beta/shelf"></include-fragment> - - - - - - <div - class="application-main " - data-commit-hovercards-enabled - data-discussion-hovercards-enabled - data-issue-and-pr-hovercards-enabled - > - <div itemscope itemtype="http://schema.org/SoftwareSourceCode" class=""> - <main id="js-repo-pjax-container" data-pjax-container > - - - - - - - - <include-fragment src="/orgs/Glogobyte/survey_banner"> - </include-fragment> - - - - <div id="repository-container-header" class="pt-3 hide-full-screen mb-5" style="background-color: var(--color-page-header-bg);" data-pjax-replace> - - <div class="d-flex mb-3 px-3 px-md-4 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<div id="readme" class="Box-body readme blob js-code-block-container p-5 p-xl-6 gist-border-0"> - <article class="markdown-body entry-content container-lg" itemprop="text"><h2><a id="user-content-isomir-tools" class="anchor" aria-hidden="true" href="#isomir-tools"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.775 3.275a.75.75 0 001.06 1.06l1.25-1.25a2 2 0 112.83 2.83l-2.5 2.5a2 2 0 01-2.83 0 .75.75 0 00-1.06 1.06 3.5 3.5 0 004.95 0l2.5-2.5a3.5 3.5 0 00-4.95-4.95l-1.25 1.25zm-4.69 9.64a2 2 0 010-2.83l2.5-2.5a2 2 0 012.83 0 .75.75 0 001.06-1.06 3.5 3.5 0 00-4.95 0l-2.5 2.5a3.5 3.5 0 004.95 4.95l1.25-1.25a.75.75 0 00-1.06-1.06l-1.25 1.25a2 2 0 01-2.83 0z"></path></svg></a>isomiR tools</h2> -<p>List of tools updated 01.01.2021</p> -<table> -<thead> -<tr> -<th align="center">Tool name</th> -<th align="center">Type</th> -<th>Tool Features</th> -<th align="center">Year</th> -<th align="center">Authors</th> -<th align="center">Journal<br>URL<br>Reference<br>(DOI number)</th> -</tr> -</thead> -<tbody> -<tr> -<td align="center">miRMaster</td> -<td align="center">Web</td> -<td>● Quantification of miRNAs and non-coding RNAs<br>● Discovering of new miRNAs and isomiRs<br>● Discovering of new miRNAs and isomiRs<br>● Quantification on known and novel miRNA with miRDeep2<br>● Preprocessing (adapter trimming, quality filtering, read collapsing)<br>● Mapping with Bowtie to various ncRNA (rRNAs, snRNAs, snoRNAs, scaRNAs, lincRNAs, piRNAs, tRNAs)<br>● Exogenous miRNAs mapping with bacteria and viruses<br>● Used for validation used samples from lung and blood samples from PAX blood RNA pool</td> -<td align="center">2017</td> -<td align="center">Tobias Fehlmann et all.</td> -<td align="center">Nucleic Acids Research<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587802/" rel="nofollow">[URL]</a><br><br>10.1093/nar/ gkx595</td> -</tr> -<tr> -<td align="center">QuickMIRSeq</td> -<td align="center">Linux</td> -<td>● Quantify miRNAs and isomiRs<br>● Avoid of multiple mapping issue of reads of identical sequences<br>● Clustering and grouping of identical and similar sequences<br>● Trimming adapters, collapsing, joint mapping with Bowtie<br>● Remapping reads with mismatches to a reference genome to further reduce the number of false hits</td> -<td align="center">2017</td> -<td align="center">Shanrong Zhao et all.</td> -<td align="center">BMC Bioinformatics<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359966/" rel="nofollow">[URL]</a><br><br>10.1186/s12859 -017-1601-4</td> -</tr> -<tr> -<td align="center">iMir</td> -<td align="center">Linux<br>Mac</td> -<td>● Identification of miRNAs and other sncRNAs, such as piRNAs<br>● Adapter trimming, quality filtering, differential expression analysis<br>● Analysis of sncRNAs and novel miRNAs<br>● Identification of isomirs using miRanalyzer<br>● Using miRAnalyzer and miRDeep2<br>● Statistical analysis to remove low expressed sncRNAs<br>● Differential Expression using Deseq Quantile normalization<br>● Target Prediction using TargetScan and miRanda</td> -<td align="center">2013</td> -<td align="center">Giorgio Giurato et all.</td> -<td align="center">BMC<br>Bioinformatics<br><br>Open access<br><br><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-362" rel="nofollow">[URL]</a><br><br>10.1186/1471 -2105-14-362</td> -</tr> -<tr> -<td align="center">MIR-isomiRExp</td> -<td align="center">Web</td> -<td>● Analyze the expression patterns or miRNA/isomer levels<br>● miRNA maturation and processing mechanism at isomiRs levels<br>● Using MirBase DB, mapping with Bowtie<br>● Differential expression using Deseq<br>● Analysis at the isomiR levels based/independent on miRNA locus<br>● Arm-switching analysis</td> -<td align="center">2016</td> -<td align="center">Li Guo et all.</td> -<td align="center">Nature<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806314/" rel="nofollow">[URL]</a><br><br>10.1038/ srep23700</td> -</tr> -<tr> -<td align="center">miRNAgFree</td> -<td align="center">Linux<br>Windows</td> -<td>● miRNA prediction based on biogenesis features (known 5’ homogeneity) and isomiR duplex forming<br>● Uses the sRNAbench preprocessing</td> -<td align="center">2017</td> -<td align="center">EL Aparicio et all.</td> -<td align="center">BioRxiv<br><br><a href="https://www.biorxiv.org/content/10.1101/193094v1.full" rel="nofollow">[URL]</a><br><br>10.1101/193094</td> -</tr> -<tr> -<td align="center">isomiRID</td> -<td align="center">Linux<br>Mac</td> -<td>● Identification of 5’, 3’ and polymorphic isomiRs<br>● Identification of non-templated 5’ or 3’ end and variations<br>● It could be applied to every organism (plants + animals)<br>● Detection of isomiRs with one mismatch<br>● Mapping in pre-miRNAs with Bowtie</td> -<td align="center">2013</td> -<td align="center">Luiz Felipe Valter de Oliveira et all.</td> -<td align="center">Bioinformatics<br><br><a href="https://academic.oup.com/bioinformatics/article/29/20/2521/276800" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ btt424</td> -</tr> -<tr> -<td align="center">MIRPIPE</td> -<td align="center">Web</td> -<td>● Rapid and simple browser-based miRNA homology detection and quantification of miRNAs<br>● Read counts from isomiRs of the same miRNA are combined. <br>● Using FASTX-tollkit, Cutadapt, BLASTN</td> -<td align="center">2014</td> -<td align="center">Carsten Kuenne et all.</td> -<td align="center">Bioinformatics<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816158/" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ btu573</td> -</tr> -<tr> -<td align="center">CASMIR</td> -<td align="center">Standalone<br>Linux</td> -<td>● Sequence-oriented isomiR annotation which allows unbiased identification of global isomiRs from small sequencing data<br>● Alignment against canonical and precursors from miRBase<br>● Discovering of canonical, 5’, 3’, polymorphic, mixed type, non-templated isomiRs, quantification using miRDeep2<br>● In-house trimming and size filtering<br>● BLAST with in house custom isomiR-BLAST alignment tool<br>● Differential expression performed with a Poisson regression model combined with a quasi-likelihood approach and AUC based on methods of DeLong and Clarke-Pearson</td> -<td align="center">2018</td> -<td align="center">Chung Wah Wu et all.</td> -<td align="center">BMC Genomics<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pubmed/29801434" rel="nofollow">[URL]</a><br><br>10.1186/s1286 4-018-4794-7</td> -</tr> -<tr> -<td align="center">IsomiR-SEA</td> -<td align="center">Linux<br>Windows<br>Mac</td> -<td>● Provide users with a complete and accurate picture of the miRNAs, isomiRs and conserved miRNA:mRNA interaction sites <br>● Provide accurate miRNA and isomiRs expression levels<br>● Use a specialized algorithm for alignment<br>● Evaluates the positions of the encountered mismatches in analyzed tags</td> -<td align="center">2016</td> -<td align="center">Gianvito Urgese et all.</td> -<td align="center">BMC Bioinformatics<br><br><a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0958-0" rel="nofollow">[URL]</a><br><br>10.1186/s12859 -016-0958-0</td> -</tr> -<tr> -<td align="center">DeAnnIso</td> -<td align="center">Web</td> -<td>● Detection and Annotation of IsomiRs from sRNA se- quencing data<br>● Еxtract the differentially expressing isomiRs with isomiRs expression, isomiRs classification from paired or multiple samples<br>● Tissue specific isomiR expression<br>● Using Bowtie and BLAST with miRBase<br>● Normalization with RPM<br>● isomiRs’ classification, 5’ isomiRs, 3’ isomiRs, isomiRs with internal modifications, templated and non-templated <br>● Target analysis and enrichment analysis of isomiRs with miRanda or RNA hybrid</td> -<td align="center">2016</td> -<td align="center">Yuanwei Zhang et all.</td> -<td align="center">Nucleic Acids Research<br><br><a href="https://www.ncbi.nlm.nih.gov/pubmed/27179030" rel="nofollow">[URL]</a><br><br>10.1093/nar/ gkw427</td> -</tr> -<tr> -<td align="center">IsomiRage</td> -<td align="center">Windows<br>Mac</td> -<td>● Identification of miRNA variants (canonical miRNAs, templated and non-templated isomiRs)<br>● Detects and groups all 3’-,5’- and trimmed variants <br>● Uses reference sequences from miRBase<br>● Classification of isomiRs according to the type of modification (uridylation, adenylation,etc)<br>● Mapping performed with Bowtie with no mismatches to reference and custom genome<br>● Normalization with RPM and read counts that can be used for comparisons of fold changes and other downstream analyses</td> -<td align="center">2014</td> -<td align="center">Muller Heiko et all.</td> -<td align="center">Frontiers in Bioengineering and Biotechnology<br><br><a href="https://www.frontiersin.org/articles/10.3389/fbioe.2014.00038/full" rel="nofollow">[URL]</a><br><br>10.3389/fbioe. 2014.00038</td> -</tr> -<tr> -<td align="center">QuagmiR</td> -<td align="center">Standalone<br>Web</td> -<td>● Designed for the detection and annotation of heterogeneous isomiRs<br>● Provide extensive customization of the process and reference databases according to user’s diverse research needs<br>● Can be used to analyze both private datasets and the public datasets that are available to authorized researchers through the CGC</td> -<td align="center">2018</td> -<td align="center">Xavier Bofill-De Ros et all.</td> -<td align="center">Bioimformatics<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499244/" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ bty843</td> -</tr> -<tr> -<td align="center">Jasmine</td> -<td align="center">R + Java</td> -<td>● Identification of isomiR populations.<br>● Propose a comprehensive isomiR nomenclature<br>● Uses curated miRBase annotation.<br>● Adapter trimming (trimmomatic, cutadapt)<br>● Collapsing trimmed reads (fastx_collapser, fastq _to_fasta from FASTX-toolkit), Quality control (FastQC)<br>● Mapping with Bowtie with at least one mismatch<br>● Uses miRBase database</td> -<td align="center">2019</td> -<td align="center">Xiangfu Zhong et all.</td> -<td align="center">Bioinformatics<br><br><a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz806/5612093" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ btz806</td> -</tr> -<tr> -<td align="center">CBS-miRSeq</td> -<td align="center">Linux<br>Docker<br>VM</td> -<td>● Color-spaced raw reads<br>● Read length distribution, summary of adapter removal, mapping statistics, and raw expression count matrix of known miRNAs.<br>● Using Bowtie with reference genome<br>● Differential expression analysis using Deseq2, EdgeR<br>● Identifies isomiRs using miRspring<br>● Predicts novel miRNA candidates using miRDeep2<br>● Predicts the most consistent miRNA:mRNA unique pairs, using RNAhybrid, miRanda</td> -<td align="center">2019</td> -<td align="center">Rupesh K. Kesharwani et all.</td> -<td align="center">Computers in Biology and Medicine<br><br><a href="https://www.sciencedirect.com/science/article/pii/S001048251930188X" rel="nofollow">[URL]</a><br><br>10.1016/ j.compbiomed. 2019.05.019.</td> -</tr> -<tr> -<td align="center">sRNAtoolbox</td> -<td align="center">Web</td> -<td>●Expression profiling of small RNAs, prediction of novel microRNAs, analysis of isomiRs<br>● Differential expression using DESeq, edgeR, and NOISeq<br>● Target prediction onuser-provided input data based on Miranda, PITA and TargetSpy<br>● Visualization of sRNA expression data in a genome context using jBrowse</td> -<td align="center">2015</td> -<td align="center">Antonio Rueda et all.</td> -<td align="center">Nucleic Acids Research<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489306/pdf/gkv555.pdf" rel="nofollow">[URL]</a><br><br>10.1093/nar/ gkv555</td> -</tr> -<tr> -<td align="center">sRNAnalyzer</td> -<td align="center">Web</td> -<td>● miRNA profiling strategies for isomiRs<br>● Detection of potential SNPs in miRNAs<br>● Uses Cutadapt, Printseq, FastX for preprocessing and Bowtie for mapping; MirBase and MirGen DB<br>● Use of LPM (local probability mapping) strategy to increase mapping specificity<br>● Extensive rRNA and tRNA filtering steps to enhance the accuracy of exogenous RNA mapping<br>● Exogenous RNA mapping process using sRNAnalyzer</td> -<td align="center">2017</td> -<td align="center">Xiaogang Wu et all.</td> -<td align="center">Nucleic Acids Research<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pubmed/29069500" rel="nofollow">[URL]</a><br><br>10.1093/nar/ gkx999</td> -</tr> -<tr> -<td align="center">mirPRo</td> -<td align="center">Linux</td> -<td>● Quantify known miRNAs<br>● Predict novel miRNAs and miRNA family expression quantification<br>● IsomiRs identification and categorization<br>● Arm switching detection<br>● Using Novoalign, HTSeq and pre-miRNAs from miRBase<br>● Using DESeq to perform differential expression profile analysis for known and novel mature miRNAs</td> -<td align="center">2015</td> -<td align="center">Jieming Shi et all.</td> -<td align="center">Nature<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4592965/" rel="nofollow">[URL]</a><br><br>10.1038/ srep14617</td> -</tr> -<tr> -<td align="center">miRge</td> -<td align="center">Standalone</td> -<td>● MirGeneDB miRNAs were used to assemble positive clusters (known miRNAs and tRNA, snoRNA, rRNA or mRNA were used to assemble negative clusters (known non-miRNAs)<br>● Identification of isomiRs<br>● Novel miRNA detection <br>● Preprocessing with Cutadapt and mapping (Bowtie)<br>● Using miRbase and miRGen DB<br>● Detection of A-to-I editing</td> -<td align="center">2015</td> -<td align="center">Alexander S. Baras et all.</td> -<td align="center">Plos one<br><br>Open Access<br><br><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143066" rel="nofollow">[URL]</a><br><br>10.1371/journal. pone.0143066</td> -</tr> -<tr> -<td align="center">miRDis</td> -<td align="center">Web</td> -<td>● Systematic annotation of known miRNAs and other noncoding RNAs based on read mapped regions <br>● Prediction of novel miRNAs and noncoding RNAs through assigning ambiguous reads to unique genome region with well-predicted RNA structure <br>● Detection of candidate exogenous miRNAs transported from dietary species<br>● Using FASTQC, Cutadapt, Bowtie and EdgeR</td> -<td align="center">2017</td> -<td align="center">Hanyuan Zhang et all.</td> -<td align="center">Briefings in Bioinformatics<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pubmed/28073746" rel="nofollow">[URL]</a><br><br>10.1093/bib/ bbw140</td> -</tr> -<tr> -<td align="center">miRMOD</td> -<td align="center">Windows</td> -<td>● Identifies and analyzes miRNA 3’ and 5’ modifications (non-templated additions as well as trimming)<br>● Using Bowtie with reference genome/pre-miRNA<br>● Provides useful statistics about various types of miRNA modifications along with its frequencies.<br>● Target alteration analysis</td> -<td align="center">2015</td> -<td align="center">Abhinav Kaushik et all.</td> -<td align="center">PeerJ<br><br>Open Access<br><br><a href="https://www.ncbi.nlm.nih.gov/pubmed/26623179" rel="nofollow">[URL]</a><br><br>10.7717/ peerj.1332</td> -</tr> -<tr> -<td align="center">mirTools 2.0</td> -<td align="center">Web</td> -<td>● Detection of various types of ncRNAs (miRNA, tRNA, snRNA, snoRNA, rRNA and piRNA)<br>● Identify miRNA-targeted genes<br>● Performs functional annotation or miRNA targets (GO, KEGG, PPI)<br>● Detect differentially expressed ncRNAs with RPM and the Bayesian method<br>● Detect novel miRNAs using miRDeep</td> -<td align="center">2013</td> -<td align="center">Jinyu Wu et all.</td> -<td align="center">RNA Biology<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849156/" rel="nofollow">[URL]</a><br><br>10.4161/ rna.25193</td> -</tr> -<tr> -<td align="center">Chimira</td> -<td align="center">Web</td> -<td>● Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences<br>● Identifies epi-transcriptomic modifications in the input sequences. <br>● Alignment with BLAST to miRbase and differential Expression of miRNAs using Deseq2<br>● Modification profiles of 3’ and 5’ and internal modifications, uridylation, adenylation and internal modifications or variations of the miRNAs.</td> -<td align="center">2015</td> -<td align="center">Dimitrios M. Vitsios et all.</td> -<td align="center">Bioinformatics<br><br><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595902/" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ btv380</td> -</tr> -<tr> -<td align="center">miRTOP</td> -<td align="center">Standalone<br>Linux</td> -<td>● Generation of a new file format mirGFF3.<br>● It is compatible with the commonly used tools output files (sRNAbench, Prost!, isomiR-SEA, OptimiR e.g.).<br>● Converts mirGFF3 file into several different types such as count matrix, FASTA and VCF formats.<br>● Open source and community-based project.</td> -<td align="center">2019</td> -<td align="center">Thomas Desvignes et all.</td> -<td align="center">Bioinformatics<br><br>Open Access<br><br><a href="https://academic.oup.com/bioinformatics/article/36/3/698/5556118" rel="nofollow">[URL]</a><br><br>10.1093/ bioinformatics/ btz675</td> -</tr> -<tr> -<td align="center">Prost!</td> -<td align="center">Standalone<br>Linux</td> -<td>● Aligns reads to a user-defined genomic dataset.<br>● Groups reads based on their potential genomic origins, seed sequence and annotation.<br>● Reports frequencies of individual sequence variations with respect to reference genome and the most expressed sequence. <br>● Uses Cutadapt and FASTX-toolkit for preprocessing, BBMap suite for alignment, MirBase for annotation and Deseq2 for differential expression.</td> -<td align="center">2019</td> -<td align="center">Thomas Desvignes et all.</td> -<td align="center">Nature<br><br>Open Access<br><br><a href="https://www.nature.com/articles/s41598-019-40361-8" rel="nofollow">[URL]</a><br><br>10.1038/ s41598-019- 40361-8</td> -</tr> -<tr> -<td align="center">OptimiR</td> -<td align="center">Standalone<br>Linux</td> -<td>● Detect genotyping errors<br>● Suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers.<br>● Uses Cutadapt for preprocessing, Bowtie2 for alignment and miRBase for annotation.<br>● Uses a scoring algorithm to identify the most plausible alignments.<br>● Produces a comparison analysis of genotype data provided by the user and the genotype data that could be inferred from the sequenced reads aligned to polymiRs</td> -<td align="center">2019</td> -<td align="center">Florian Thibord et all.</td> -<td align="center">Bioinformatics<br><br>Open Access<br><br><a href="https://rnajournal.cshlp.org/content/early/2019/02/28/rna.069708.118" rel="nofollow">[URL]</a><br><br>10.1261/ rna.069708.118</td> -</tr> -<tr> -<td align="center">isomiRs: Analyze isomiRs and miRNAs from small RNA-seq</td> -<td align="center">R library</td> -<td>● Uses as input file the count matrix<br>● Includes various functions for characterization of miRNAs and isomiRs, clustering, differential expression and visualizations.<br>● Designed to analyze the output of SeqBuster tool or any other tool after converting to the desire format<br>● user can control the analysis step by step.</td> -<td align="center">2020</td> -<td align="center">Pantano L, Escaramis G</td> -<td align="center">Bioconductor<br><br><a href="http://bioconductor.org/packages/release/bioc/html/isomiRs.html" rel="nofollow">[URL]</a><br><br>10.18129/ B9.bioc.isomiRs</td> -</tr> -</tbody> -</table> -</article> - 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