IGVF

/software-versions/cellranger-v6.0.1/

released

fbd5e8fb-4206-4b43-92d6-922cdfe1338b

/analysis-step-versions/f9f6ae88-d515-4e49-9902-deea3cf87703/

/analysis-steps/IGVFWF8837BHJV-gersbach-facs-crispr-screen-alignment-step/

Gersbach FACS CRISPR screen Alignment Step

/software-versions/bowtie2-v2.3.5/

released

f9f6ae88-d515-4e49-9902-deea3cf87703

/analysis-step-versions/f53cadd0-3e88-4b35-ab64-8e1683998686/

/analysis-steps/IGVFWF6270QWBB-gersbach-ggr-rna-seq-pipeline-quantification-step/

Gersbach GGR RNA-seq Pipeline Quantification Step

/software-versions/bamtools-v2.2.3/

released

f53cadd0-3e88-4b35-ab64-8e1683998686

/analysis-step-versions/f50466f8-1ed0-4abc-8604-f6668678139f/

luca-pinello:crispr-bean-mapped-counts-generation-step

/analysis-steps/IGVFWF8641DTYD-crispr-bean-mapped-counts-generation-step/

CRISPR-BEAN mapped counts generation step

/awards/HG012010/

/labs/luca-pinello/

/software-versions/crispr-bean-v1.2.8/

released

f50466f8-1ed0-4abc-8604-f6668678139f

/analysis-step-versions/f24bbbaf-4b85-4f27-bc11-d6527da766e2/

/analysis-steps/IGVFWF7196TNJP-scatac-seq-fragment-alignment-step/

scATAC-seq fragment alignment step

/software-versions/scATAC-processing-v1.0.0/

/labs/jay-shendure/

released

f24bbbaf-4b85-4f27-bc11-d6527da766e2

/analysis-step-versions/f177d6b8-48b1-4d58-af7c-5c50da2b0e25/

/analysis-steps/IGVFWF3101OPAH-bluestarr-training-prediction-step/

BlueSTARR training and prediction step

/awards/HG011967/

/labs/andrew-allen/

/software-versions/bluestarr-v0.1.1/

released

f177d6b8-48b1-4d58-af7c-5c50da2b0e25

/analysis-step-versions/ed0d80a9-1fc7-484a-9668-750558fc383d/

harinder-singh:perturbation-scRNAseq-pipeline-mira-processing-step-v1

/analysis-steps/IGVFWF0081UKFO-perturbation-scrnaseq-pipeline-mira-processing-step/

Singh Perturbation Single Cell RNA-seq MIRA Processing Step

/awards/HG012041/

/labs/harinder-singh/

/software-versions/mira-v2.1.0/, /software-versions/scanpy-v1.10.0/

released

ed0d80a9-1fc7-484a-9668-750558fc383d

/analysis-step-versions/ea59af97-e192-40b0-9699-909a8b3baa56/

/analysis-steps/IGVFWF1390CSVD-mpranalyze-variant-annotation-step/

MPRAnalyze Variant Annotation Step

/software-versions/mpranalyze-v1.24.0/

/labs/nadav-ahituv/

released

ea59af97-e192-40b0-9699-909a8b3baa56

/analysis-step-versions/e904b252-f348-4c6d-835c-5ae6bf91b9a0/

harinder-singh:multiome-pipeline-cellranger-arc-step-v1

/analysis-steps/IGVFWF8495CUNO-multiome-pipeline-cellranger-arc-step/

Singh Single Cell Multiome CellRanger ARC Step

/awards/HG012041/

/labs/harinder-singh/

/software-versions/cellranger-arc-v2.0.2/

released

e904b252-f348-4c6d-835c-5ae6bf91b9a0

/analysis-step-versions/e27a16d2-c700-405f-92c4-89efe1a558ce/

jason-buenrostro:share-seq-alignment-v2-fragment-genration-step-version

/analysis-steps/IGVFWF0507XZOR-share-seq-alignment-v2-fragment-genration-step/

SHARE-seq alignment v2 fragment generation step

/awards/HG011986/

/labs/jason-buenrostro/

/software-versions/fastq-process-v0.9.0/, /software-versions/gnu-parallel-v20161222.0.0/, /software-versions/samtools-v1.21.0/, /software-versions/bowtie2-v2.5.4/, /software-versions/bedtools-v2.26.0/, /software-versions/tabix-v1.10.2/

released

e27a16d2-c700-405f-92c4-89efe1a558ce

/analysis-step-versions/dca2aa98-db85-449c-93f3-3f409a12f051/

luca-pinello:crispr-bean-modeling-step

/analysis-steps/IGVFWF8641DTYD-crispr-bean-modeling-step/

CRISPR-BEAN modeling step

/awards/HG012010/

/labs/luca-pinello/

/software-versions/crispr-bean-v1.2.8/

released

dca2aa98-db85-449c-93f3-3f409a12f051

/analysis-step-versions/cfaab400-714a-45b5-9800-3ff6f9c929c2/

/analysis-steps/IGVFWF6957ZNII-superstarr-alignment-step/

SUPERSTARR Alignment step

/software-versions/samtools-v2.5.1/, /software-versions/bowtie2-v1.1.0/, /software-versions/reddy-starrseq-read-processing-v1.0.0/

/labs/tim-reddy/

released

cfaab400-714a-45b5-9800-3ff6f9c929c2

/analysis-step-versions/c95d766a-a900-4694-8065-e12651f618ba/

/analysis-steps/IGVFWF6411VZLF-gersbach-ggr-atac-seq-pipeline-alignment-step/

Gersbach GGR ATAC-seq Pipeline Alignment Step

/software-versions/bowtie-v1.2.3/, /software-versions/samtools-v1.3.0/

released

c95d766a-a900-4694-8065-e12651f618ba

/analysis-step-versions/c8de4554-6fda-4373-aa41-5574220df999/

/analysis-steps/IGVFWF6957ZNII-superstarr-variant-quantification-step/

SUPERSTARR Variant Quantification Step

/software-versions/samtools-v1.3.0/, /software-versions/pandas-v1.4.0/, /software-versions/bird-v1.0.0/

released

c8de4554-6fda-4373-aa41-5574220df999

/analysis-step-versions/c3d281e0-f647-4d3c-8ed5-710329d183f2/

/analysis-steps/IGVFWF1905PJEA-scrispra-differential-analysis-step/

scCRISPRa differential analysis step

/software-versions/sceptre-v0.9.2/

/labs/jay-shendure/

released

c3d281e0-f647-4d3c-8ed5-710329d183f2

/analysis-step-versions/c3ad4525-87d0-4d22-9410-f3e616d7cb9c/

/analysis-steps/IGVFWF6032PEGT-mprasnakeflow-quantification-step/

MPRAsnakeflow Quantification Step

/software-versions/mprasnakeflow-quantification-v0.3.0/

/labs/martin-kircher/

released

c3ad4525-87d0-4d22-9410-f3e616d7cb9c

/analysis-step-versions/c0fbe877-fa6c-423b-8d56-e600bf8e2859/

daniel-bauer:mageck-mapped-counts-generation-step

/analysis-steps/IGVFWF7224ABWD-mageck-mapped-counts-generation-step/

MAGeCK mapped counts generation step

/awards/HG012010/

/labs/daniel-bauer/

/software-versions/mageck-v0.5.9.5/

released

c0fbe877-fa6c-423b-8d56-e600bf8e2859

/analysis-step-versions/b4bb30ef-db5c-4314-bc56-a9f536851ec2/

/analysis-steps/IGVFWF1905PJEA-scrispra-differential-analysis-step/

scCRISPRa differential analysis step

/software-versions/shendure-sccrispra-custom-seurat-scripts-v1.0.0/

/labs/jay-shendure/

released

b4bb30ef-db5c-4314-bc56-a9f536851ec2

/analysis-step-versions/b1581dec-2980-4a2e-8884-4e95219da4d4/

jesse-engreitz:Variant-EFFECTS_pipeline-variant-effect-on-expression-quantification_step_v1.0.0

/analysis-steps/IGVFWF0099SJHI-variant-effects-pipeline-variant-effect-on-expression-quantification-step/

Variant-EFFECTS_pipeline_variant-effect-on-expression-quantification_step

/awards/HG011972/

/labs/jesse-engreitz/

/software-versions/engreitz%20variant-effects%20scripts-v1.0.0/

preview

b1581dec-2980-4a2e-8884-4e95219da4d4

/analysis-step-versions/a958f5b0-0c40-46ec-82e9-db6b2b849244/

/analysis-steps/IGVFWF7562QXLM-count-matrix-generation-step/

Count Matrix Generation Step

/software-versions/cellranger-v6.0.1/

released

a958f5b0-0c40-46ec-82e9-db6b2b849244

/analysis-step-versions/a6d3968e-0580-4ec7-90a2-541324156967/

/analysis-steps/IGVFWF6270QWBB-gersbach-ggr-rna-seq-pipeline-signal-step/

Gersbach GGR RNA-seq Pipeline Signal Generation Step

/software-versions/deseq2-v1.36.0/

released

a6d3968e-0580-4ec7-90a2-541324156967

/analysis-step-versions/9c457b9f-fc6d-4cf1-b249-218827e9b449/

igvf:single-cell-uniform-pipeline-kalliso-bustools-rnaseq-step-v1

/analysis-steps/IGVFWF7365VWQV-single-cell-uniform-pipeline-kalliso-bustools-rnaseq-step/

Kallisto Bustools RNAseq Processing for Single Cell Uniform Pipeline Step

/software-versions/igvf-kallisto-bustools-v1.0.0/

released

9c457b9f-fc6d-4cf1-b249-218827e9b449

/analysis-step-versions/8ce84c63-40fd-4894-b163-044a613fe53c/

harinder-singh:scRNAseq-pipeline-cellranger-matrix-generation-step-v1

/analysis-steps/IGVFWF8690BLTY-singh-scrnaseq-pipeline-cellranger-matrix-generation-step/

Singh Single Cell RNA-seq CellRanger Matrix Generation Step

/awards/HG012041/

/labs/harinder-singh/

/software-versions/cellranger-v7.0.1/

released

8ce84c63-40fd-4894-b163-044a613fe53c

/analysis-step-versions/886b365e-3105-424a-8972-7476238b54d7/

/analysis-steps/IGVFWF8837BHJV-gersbach-facs-crispr-screen-quantification-step/

Gersbach FACS CRISPR screen Quantification Step

/software-versions/samtools-v1.3.1/

released

886b365e-3105-424a-8972-7476238b54d7

/analysis-step-versions/85a076e7-4167-4a08-a523-905fc3ee1b8b/

/analysis-steps/IGVFWF6032PEGT-mprasnakeflow-assignment-step/

MPRAsnakeflow Assignment Step