biobenkj

compartmap

Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

biscuit

BISulfite-seq CUI Toolkit

biscuiteer

tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output

bisplotti

Plotting package for bisulfite sequencing and methylation arrays

bonito

Bonito - A PyTorch Basecaller for Oxford Nanopore Reads

boostme

R package to impute methylation within WGBS using machine learning

bsseq

Devel repository for bsseq

compartmap_manuscript

This repository contains all the code and much of the processed data for the compartmap manuscript

complexion

R utilities to compute library complexity measures

covmat

Package Development for GSOC 2015

datasets

Datasets related to the IGVF workflows

densvis

R package implementing the density-preserving data visualization tools den-SNE and densMAP

kallisto

Near-optimal RNA-Seq quantification

kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

MTseeker

mitochondrial variant analysis tools

myfirstrepo

This is for VAIGS 2021 bioinformatics course git session

ngs-tools

Reusable tools for working with next-generation sequencing (NGS) data

QDNAseq_bin_annotations

This repo contains bin annotations for QDNAseq CNA calling

seqspec

sleuth

Differential analysis of RNA-Seq

spiky

stormseq_protocols

This repository contains the current STORM-seq protocol for library construction and analysis

synthbar

Add synthetic cell barcode to FASTQ reads

TCGA_TGCT_metharray_analysis

This repository contains public analysis scripts for processing and producing figures for the TCGA TGCT cohort

TE_expression_in_scRNAseq

vaigs_teaching

velocessor

velocity processor

WGBS_Biscuit_Snakemake

Snakemake Workflow For WGBS Data

wzmetagene

Create sub-intervals from intervals