Mercurial > repos > galaxyp > msstatstmt

comparison msstatstmt.xml @ 5:a5e394b36d87 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt commit 909dc08cad859acb747324c8c867770022a2a455"
author galaxyp
date Wed, 11 Aug 2021 11:11:22 +0000
parents 8375a0035d79
children bd1535813cfe
comparison
equal deleted inserted replaced
4:8375a0035d79 5:a5e394b36d87
562 <help><![CDATA[ 562 <help><![CDATA[
563 MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance. 563 MSstatsTMT is an R-based package for detecting differentially abundant proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling. It is applicable to isobaric labeling quantitative proteomics, including iTRAQ and TMT data. MSstatsTMT provides functionalities for two types of analysis: 1) Protein summarization based on peptide quantification data and visualization; 2) Model-based group comparison to detect significant changes in abundance.
564 564
565 **Notes** 565 **Notes**
566 566
567 - MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required. 567 - MSstatsTMT 11 column format: For TMT datasets an additional 'Channel' column is required, which has to be in the format 'channel.X' with X being the channel number..
568 568
569 :: 569 ::
570 570
571 #> ProteinName PeptideSequence 571 #> ProteinName PeptideSequence
572 #> 1 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR 572 #> 1 sp|Q60854|SPB6_MOUSE .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR
580 #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 580 #> 2 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
581 #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 581 #> 3 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
582 #> 4 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 582 #> 4 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
583 #> 5 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 583 #> 5 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
584 #> 6 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3 584 #> 6 3 .(TMT6plex)AFVEVNEEGTEAAAATAGMM(Oxidation)TVR_3 3
585 #> TechRepMixture Run Channel BioReplicate Condition Intensity 585 #> TechRepMixture Run Channel BioReplicate Condition Intensity
586 #> 1 3_3 3_3_3 1 21 Long_HF NA 586 #> 1 3_3 3_3_3 channel.1 21 Long_HF NA
587 #> 2 3_3 3_3_3 2 22 Norm 1068.580 587 #> 2 3_3 3_3_3 channel.2 22 Norm 1068.580
588 #> 3 3_3 3_3_3 3 23 Long_M 1508.330 588 #> 3 3_3 3_3_3 channel.3 23 Long_M 1508.330
589 #> 4 3_3 3_3_3 4 24 Long_HF NA 589 #> 4 3_3 3_3_3 channel.4 24 Long_HF NA
590 #> 5 3_3 3_3_3 5 25 Long_LF 1580.951 590 #> 5 3_3 3_3_3 channel.5 25 Long_LF 1580.951
591 #> 6 3_3 3_3_3 6 26 Long_HF 1820.072 591 #> 6 3_3 3_3_3 channel.6 26 Long_HF 1820.072
592 592
593 For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_ 593 For more information please visit the `MSstatsConvert documentation <https://bioconductor.org/packages/devel/bioc/vignettes/MSstatsConvert/inst/doc/msstats_data_format.html>`_
594 594
595 - Comparison matrix as tabular file 595 - Comparison matrix as tabular file
596 596
617 G1+G2-G5 0.5 0.5 0 0 -1 617 G1+G2-G5 0.5 0.5 0 0 -1
618 618
619 For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_ 619 For additional help please visit the `MSstatsTMT documentation <https://msstats.org/msstatstmt/>`_
620 ]]> 620 ]]>
621 </help> 621 </help>
622
622 <citations> 623 <citations>
623 <citation type="doi">10.1074/mcp.ra120.002105</citation> 624 <citation type="doi">10.1074/mcp.ra120.002105</citation>
624 </citations> 625 </citations>
625 </tool> 626 </tool>