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58 items
  • AnalysisStepVersion
    fbd5e8fb-4206-4b43-92d6-922cdfe1338b
    Count Matrix Filtering Step Version
    External Lab, Community
    Software Versions
    cellranger-v6.0.1
    released
  • AnalysisStepVersion
    f9f6ae88-d515-4e49-9902-deea3cf87703
    Gersbach FACS CRISPR screen Alignment Step Version
    Charles Gersbach, Duke
    Software Versions
    bowtie2-v2.3.5
    released
  • AnalysisStepVersion
    f53cadd0-3e88-4b35-ab64-8e1683998686
    Gersbach GGR RNA-seq Pipeline Quantification Step Version
    Charles Gersbach, Duke
    Software Versions
    bamtools-v2.2.3
    released
  • AnalysisStepVersion
    f50466f8-1ed0-4abc-8604-f6668678139f
    CRISPR-BEAN mapped counts generation step Version
    Luca Pinello, MGH
    Software Versions
    crispr-bean-v1.2.8
    released
  • AnalysisStepVersion
    f24bbbaf-4b85-4f27-bc11-d6527da766e2
    scATAC-seq fragment alignment step Version
    Jay Shendure, UW
    Software Versions
    scATAC-processing-v1.0.0
    released
  • AnalysisStepVersion
    f177d6b8-48b1-4d58-af7c-5c50da2b0e25
    BlueSTARR training and prediction step Version
    Andrew Allen, Duke
    Software Versions
    bluestarr-v0.1.1
    released
  • AnalysisStepVersion
    ed0d80a9-1fc7-484a-9668-750558fc383d
    Singh Perturbation Single Cell RNA-seq MIRA Processing Step Version
    Harinder Singh, University of Pittsburgh
    Software Versions
    mira-v2.1.0, scanpy-v1.10.0
    released
  • AnalysisStepVersion
    ea59af97-e192-40b0-9699-909a8b3baa56
    MPRAnalyze Variant Annotation Step Version
    Nadav Ahituv, UCSF
    Software Versions
    mpranalyze-v1.24.0
    released
  • AnalysisStepVersion
    e904b252-f348-4c6d-835c-5ae6bf91b9a0
    Singh Single Cell Multiome CellRanger ARC Step Version
    Harinder Singh, University of Pittsburgh
    Software Versions
    cellranger-arc-v2.0.2
    released
  • AnalysisStepVersion
    e27a16d2-c700-405f-92c4-89efe1a558ce
    SHARE-seq alignment v2 fragment generation step Version
    Jason Buenrostro, Broad
    Software Versions
    fastq-process-v0.9.0, gnu-parallel-v20161222.0.0, samtools-v1.21.0, bowtie2-v2.5.4, bedtools-v2.26.0, tabix-v1.10.2
    released
  • AnalysisStepVersion
    dca2aa98-db85-449c-93f3-3f409a12f051
    CRISPR-BEAN modeling step Version
    Luca Pinello, MGH
    Software Versions
    crispr-bean-v1.2.8
    released
  • AnalysisStepVersion
    cfaab400-714a-45b5-9800-3ff6f9c929c2
    SUPERSTARR Alignment step Version
    Tim Reddy, Duke
    Software Versions
    samtools-v2.5.1, bowtie2-v1.1.0, reddy-starrseq-read-processing-v1.0.0
    released
  • AnalysisStepVersion
    c95d766a-a900-4694-8065-e12651f618ba
    Gersbach GGR ATAC-seq Pipeline Alignment Step Version
    External Lab, Community
    Software Versions
    bowtie-v1.2.3, samtools-v1.3.0
    released
  • AnalysisStepVersion
    c8de4554-6fda-4373-aa41-5574220df999
    SUPERSTARR Variant Quantification Step Version
    Charles Gersbach, Duke
    Software Versions
    samtools-v1.3.0, pandas-v1.4.0, bird-v1.0.0
    released
  • AnalysisStepVersion
    c3d281e0-f647-4d3c-8ed5-710329d183f2
    scCRISPRa differential analysis step Version
    Jay Shendure, UW
    Software Versions
    sceptre-v0.9.2
    released
  • AnalysisStepVersion
    c3ad4525-87d0-4d22-9410-f3e616d7cb9c
    MPRAsnakeflow Quantification Step Version
    Martin Kircher, BIH
    Software Versions
    mprasnakeflow-quantification-v0.3.0
    released
  • AnalysisStepVersion
    c0fbe877-fa6c-423b-8d56-e600bf8e2859
    MAGeCK mapped counts generation step Version
    Daniel Bauer, HSCI
    Software Versions
    mageck-v0.5.9.5
    released
  • AnalysisStepVersion
    b4bb30ef-db5c-4314-bc56-a9f536851ec2
    scCRISPRa differential analysis step Version
    Jay Shendure, UW
    Software Versions
    shendure-sccrispra-custom-seurat-scripts-v1.0.0
    released
  • AnalysisStepVersion
    b1581dec-2980-4a2e-8884-4e95219da4d4
    Variant-EFFECTS_pipeline_variant-effect-on-expression-quantification_step Version
    Jesse Engreitz, Stanford
    Software Versions
    engreitz variant-effects scripts-v1.0.0
    preview
  • AnalysisStepVersion
    a958f5b0-0c40-46ec-82e9-db6b2b849244
    Count Matrix Generation Step Version
    External Lab, Community
    Software Versions
    cellranger-v6.0.1
    released
  • AnalysisStepVersion
    a6d3968e-0580-4ec7-90a2-541324156967
    Gersbach GGR RNA-seq Pipeline Signal Generation Step Version
    Charles Gersbach, Duke
    Software Versions
    deseq2-v1.36.0
    released
  • AnalysisStepVersion
    9c457b9f-fc6d-4cf1-b249-218827e9b449
    Kallisto Bustools RNAseq Processing for Single Cell Uniform Pipeline Step Version
    External Lab, Community
    Software Versions
    igvf-kallisto-bustools-v1.0.0
    released
  • AnalysisStepVersion
    8ce84c63-40fd-4894-b163-044a613fe53c
    Singh Single Cell RNA-seq CellRanger Matrix Generation Step Version
    Harinder Singh, University of Pittsburgh
    Software Versions
    cellranger-v7.0.1
    released
  • AnalysisStepVersion
    886b365e-3105-424a-8972-7476238b54d7
    Gersbach FACS CRISPR screen Quantification Step Version
    Charles Gersbach, Duke
    Software Versions
    samtools-v1.3.1
    released
  • AnalysisStepVersion
    85a076e7-4167-4a08-a523-905fc3ee1b8b
    MPRAsnakeflow Assignment Step Version
    Martin Kircher, BIH
    Software Versions
    mprasnakeflow-assignment-v0.3.0
    released