Showing 13 of 13 results

• 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

  DPL126DIZ

  active

  Pipeline holder for unknown or undefined pipeline

• Pipeline

  DPL005RCG

  active

  A short overview of the main analysis steps for eQTL Catalogue

  Assays: RNA-seq, whole genome sequencing assay

  Software: RNA-seq quantification: eQTL-Catalogue/rnaseq, Gene expression QC and normalisation: eQTL-Catalogue/qcnorm, Genotype QC and imputation: eQTL-Catalogue/genimpute, Association testing and fine mapping: eQTL-Catalogue/qtlmap

• 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

  DPL961ZQY

  active

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

  Assays: ATAC-seq

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

• Pipeline

  DPL172PKH

  active

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

  Assays: RNA-seq

  Software: STAR, RSEM

• Pipeline

  DPL930NXT

  active

  DNase-seq Pipeline (ENCODE)

  Assays: DNase-seq

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

• Pipeline

  DPL450NWL

  active

  RNA-seq Pipeline Cebola Lab

  Assays: RNA-seq

  Software: fastp, STAR, SALMON, Samtools, deepTools

• Pipeline

  DPL610SXT

  active

  RNA-seq Pipeline (Paired-ended, ENCODE)

  Assays: RNA-seq

  Software: STAR, bedGraphToBigWig, RSEM

• Pipeline

  DPL610SXTsingleended

  active

  RNA-seq Pipeline (Single-ended, ENCODE)

  Assays: RNA-seq

  Software: STAR, RSEM, bedGraphToBigWig