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"planemo upload commit ff0d185541dc4b0a5839fca166f1beb459dee61c"
author gaelcge
date Tue, 02 Aug 2022 19:42:44 +0000
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1 ***** links to input data for 10X single-analysis and Seurat tutorials ****
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2 ****
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4 ***** Single-Cell ATACseq (10X Genomics) - from fastq to dimentionality reduction
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6 Fastq = https://support.10xgenomics.com/single-cell-atac/datasets/1.2.0/atac_v1_pbmc_5k
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7 small_fastq_files = https://support.10xgenomics.com/single-cell-atac/datasets/2.0.0/atac_pbmc_500_nextgem
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9 Software = Cell Ranger ATAC 1.2.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/installation)
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11 Tutorial from cell ranger output to clustering = https://satijalab.org/signac/articles/pbmc_vignette.html
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15 ****** Multiome (ARC) = scRNA + scATACseq (10X Genomics) - from fastq to dimentionality reduction
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17 Fastq = https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_unsorted_3k
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19 Software = Cell Ranger ARC 1.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/installation)
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21 Tutorial from cell ranger output to clustering (PBMC - RNA & ATAC) = https://satijalab.org/seurat/v4.0/weighted_nearest_neighbor_analysis.html
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25 ********** Pipeline implentation *********
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26 *******
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28 ***** Galaxy
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32 ***** NextFlow
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33 https://github.com/WarrenLab/single-cell
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34 https://figshare.com/articles/BICF_Cellranger_count_Analysis_Workflow/9702698
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35 https://nf-co.re/scrnaseq/1.0.0
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36 https://hub.docker.com/r/nfcore/demultiplex
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