Agent
Execute ENCODE ATAC-seq pipeline from FASTQ to accessibility peaks with Tn5 correction, Bowtie2, and MACS2.
24 1mo ago A 34 tokens
AGPL-3.0
24Stars on the repository
60Mods indexed here, across every type
1mo agoLast push, which is what freshness is scored on
AGPL-3.0Licence, which decides whether bodies are shown
Agent
Execute ENCODE ChIP-seq pipeline from FASTQ to peaks and signal tracks using BWA-MEM, MACS2, and IDR.
24 1mo ago A 34 tokens
AGPL-3.0
Agent
Execute CUT&RUN pipeline from FASTQ to peaks with Bowtie2, SEACR, and spike-in normalization.
24 1mo ago A 29 tokens
AGPL-3.0
Agent
Execute ENCODE DNase-seq pipeline from FASTQ to hotspots and footprints using BWA, Hotspot2, and HINT-ATAC.
24 1mo ago A 36 tokens
AGPL-3.0
hic-pipeline
05Agent
Execute ENCODE Hi-C pipeline from FASTQ to contact matrices and loop calls using BWA, pairtools, Juicer, and HiCCUPS.
24 1mo ago A 33 tokens
AGPL-3.0
Agent
Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto.
24 1mo ago A 31 tokens
AGPL-3.0
Agent
Execute ENCODE WGBS pipeline from FASTQ to methylation calls using Bismark and MethylDackel.
24 1mo ago A 29 tokens
AGPL-3.0