Showing 19 of 27 results

• Pipeline

  DPL857456

  active

  Peak Alignment Pipeline

  Assays: ATAC-seq

  Software: Peak alignment

• Pipeline

  DPL255HPT

  active

  scRNA-seq clustering for HPAP dataset

• Pipeline

  DPL066WNI

  active

  Pseudo-bulk gene expression and differential activity (Elgamal et al.)

  Assays: single cell isolation followed by RNA-seq

• Pipeline

  DPL472KCS

  active

  Annotation pipeline popularVote (popV for short) from Tabula Sapiens

  Assays: single cell isolation followed by RNA-seq

• Pipeline

  DPL269LNG

  active

  RNA-seq Pipeline 2 (Single-ended, ENCODE)

  Assays: RNA-seq

  Software: RNA pipelines, lrna-index-tophat, TopHat, Bowtie 2, lrna-align-tophat-se, Concat-fastq, Samtools, lrna-signals-unstranded, bedGraphToBigWig, STAR, lrna-signals, lrna-index-star, lrna-index-rsem, RSEM, lrna-align-star-se, lrna-quantification, lrna-mad-qc, Median Absolute Deviation

• Pipeline

  DPL009OFN

  active

  RNA-seq Pipeline 2 (Paired-ended, ENCODE)

  Assays: RNA-seq

  Software: RNA pipelines, lrna-index-tophat, TopHat, Bowtie 2, lrna-align-tophat-pe, Concat-fastq, Tophat BAM Repair, lrna-signals, bedGraphToBigWig, STAR, lrna-signals-stranded, lrna-index-star, lrna-index-rsem, RSEM, lrna-align-star-pe, Samtools, lrna-quantification, lrna-mad-qc, Median Absolute Deviation

• Pipeline

  DPL608JFY

  active

  TF ChIP-seq Pipeline 2 (ENCODE unreplicated)

  Assays: ChIP-seq, Mint-ChIP-seq

  Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, MACS2, BEDTools, Irreproducible Discovery Rate (IDR), Phantompeakqualtools, bedToBigBed

• Pipeline

  DPL721SCW

  active

  Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)

  Assays: ChIP-seq, Mint-ChIP-seq

  Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, overlap_peaks.py, bedToBigBed, MACS2, BEDTools

• Pipeline

  DPL961ZQY

  active

  ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953

  Assays: ATAC-seq

  Software: Trim Galore, BWA, Samtools, Picard, MACS2

• Pipeline

  DPL930NXT

  active

  DNase-seq Pipeline (ENCODE)

  Assays: DNase-seq

  Software: hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed

• Pipeline

  DPL064PJG

  active

  Histone ChIP-seq Pipeline 2 (ENCODE replicated)

  Assays: ChIP-seq, Mint-ChIP-seq

  Software: Bowtie 2, Samtools, sambamba, cutadapt, Picard, ptools_bin, MACS2, BEDTools, overlap_peaks.py, bedToBigBed

• Pipeline

  DPL707AXE

  active

  ATAC-seq Pipeline (ENCODE replicated)

  Assays: ATAC-seq

  Software: Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools

• Pipeline

  DPL779IGH

  active

  ATAC-seq Pipeline Cebola Lab (Hepatocytes)

  Assays: ATAC-seq

  Software: fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig

• Pipeline

  DPL741HGX

  active

  ATAC-seq Pipeline Cebola Lab

  Assays: ATAC-seq

  Software: fastp, Bowtie 2, Samtools, Picard, BEDTools, deepTools, MACS2, bedGraphToBigWig

• Pipeline

  DPL450NWL

  active

  RNA-seq Pipeline Cebola Lab

  Assays: RNA-seq

  Software: fastp, STAR, SALMON, Samtools, deepTools

• Pipeline

  DPL245EPK

  active

  ChIP-seq Pipeline Cebola Lab

  Assays: ChIP-seq

  Software: fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig

• Pipeline

  DPL403RWM

  active

  ChIP-seq Pipeline (ENCODE)

  Assays: ChIP-seq

  Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, MACS2, BEDTools, overlap_peaks.py, bedToBigBed

• Pipeline

  DPL610SXT

  active

  RNA-seq Pipeline (Paired-ended, ENCODE)

  Assays: RNA-seq

  Software: STAR, bedGraphToBigWig, RSEM

• Pipeline

  DPL983WYV

  active

  ChIP-Atlas Pipeline

  Assays: ChIP-seq, DNase-seq

  Software: SRA_Toolkit, Bowtie 2, Samtools, BEDTools, bedGraphToBigWig, MACS2, unknown, CoLo