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hicar

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

hicar_doc

hicar_tools

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

hicounts

Find overlaps for pairs in high resolution

hicvenndiagram

hmmt

R package for Hidden Markov Models with t emissions

hmmtbroadpeak

call broad peak by a modified Baum_Welch algorithm that supports multi-dimensional Student's t emission.

igv

R package for include igv.js into Rmd file

inpas

Identification of Novel alternative PolyAdenylation Sites (PAS)

jianhong.github.io

merip

mintchip

pipeline for MintChIP

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

motifstack

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

motifstack.documentation

documentation of motifStack

motifstackworkshop

workshop for motifStack

multi2one

alignment multiple fasta files to one template

nadfinder

Call wide peaks for sequencing data

nascent

Nascent Transcription Processing Pipeline

nextflowtutorial

nextflow introduction

nf-core-hicar

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts. The hyperlink here is an example of multiQC report page.

pairedtag

A snakemake workflow for single-cell multiomic data analysis pipeline

primerdesigner

pipeline for primer3

prj_dd04xq

collection of code for project DD04X

proseq

pipline for proseq

ratte

The use of RnA-seq for AnnoTation of Transpose Elements

ribosomeprofilingqc

An R package for quality assessment of ribosome profiling

rnaseq

RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

rrbseq

RRBSeq, a Bioconductor package

scrna-recom

collected resource for scRNA-seq analysis