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alleva_et_al_2021_analytic_pipeline

Analytic pipeline for long read genotyping of human PRDM9 (Alleva et al., 2021)

callhotspotsssds

Pipeline to call DSB hotspots and estimate strength from single-stranded DNA sequencing (SSDS) data.

callssdspeaks

Peak calling pipeline for SSDS data

configs

Config files used to define parameters specific to compute environments at different Institutions

cs-video-courses

List of Computer Science courses with video lectures.

genotype_prdm9_lr

Genotype PRDM9 from long read amplicon sequencing

github-actions-for-ci

hic

Analysis of Chromosome Conformation Capture data (Hi-C)

hic-pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

hicrep

Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support

kevbrick.github.io

Build a Jekyll blog in minutes, without touching the command line.

lametal2019

Analytic pipeline for Lam et al. 2019

mahgoub2020

Analytic pipeline for Mahgoub et al. 2020 (Zcwpw1)

markdown-cv

a simple template to write your CV in a readable markdown file and use CSS to publish/print it.

mihola2021

Analyses for Mihola et al paper (rat DSB hotspots) 2021

modules

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

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

multiqc_testdata

Test data for MultiQC. See https://github.com/ewels/MultiQC

pipeit

pratto_et_al_2021_analytic_pipeline

Analytic pipeline for Pratto et al. 2020

prdm9_ts

Infer template switches between parental alleles of PRDM9

random_files

Random_files

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rtseqpipeline

Pipeline to infer replication timing from WGS data.

rtsim

Replication timing simulation in mammalian genomes

ssds

Single-stranded DNA Sequencing (SSDS) nf-core pipeline

ssds_multiqc

MultiQC with SSDS module

ssds_nfcore

nf-core implementation of the SSDS pipeline

ssdsnextflowpipeline

Nextflow version of the SSDS pipeline

ssdspipeline

Sequence alignment pipeline for ssDNA sequencing (SSDS) (Khil et al., Genome Res. 2012)