Pinned Repositories
ATACseeker
ATACseq tools for Bioconductor
compartmap
Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
giab_data_indexes
This repository contains data indexes from NIST's Genome in a Bottle project.
P1_04_DMRcate-Annotation
P1 methylation data processing DMRcate, network analysis and annotation
platetools
An R package for plotting 96 / 384 / 1536 well plates
sparseMatrixUtils
Small utility package to work with sparse matrices in R
SPARTA-teaching
Teaching bacterial RNA-seq with SPARTA
SPARTA_Linux
SPARTA_Mac
vari_teaching_homepage
Homepage for VARI workshops
biobenkj's Repositories
biobenkj/compartmap
Reconstruction of higher order chromatin from scRNA-seq and scATAC-seq
biobenkj/ArchR
ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
biobenkj/biscuit
BISulfite-seq CUI Toolkit
biobenkj/biscuiteer
tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output
biobenkj/bisplotti
Plotting package for bisulfite sequencing and methylation arrays
biobenkj/bonito
Bonito - A PyTorch Basecaller for Oxford Nanopore Reads
biobenkj/boostme
R package to impute methylation within WGBS using machine learning
biobenkj/bsseq
Devel repository for bsseq
biobenkj/compartmap_manuscript
This repository contains all the code and much of the processed data for the compartmap manuscript
biobenkj/covmat
Package Development for GSOC 2015
biobenkj/datasets
Datasets related to the IGVF workflows
biobenkj/densvis
R package implementing the density-preserving data visualization tools den-SNE and densMAP
biobenkj/how_are_we_stranded_here
Check strandedness of RNA-Seq fastq files
biobenkj/kallisto
Near-optimal RNA-Seq quantification
biobenkj/kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
biobenkj/mgatk
mgatk: mitochondrial genome analysis toolkit
biobenkj/MTseeker
mitochondrial variant analysis tools
biobenkj/myfirstrepo
This is for VAIGS 2021 bioinformatics course git session
biobenkj/ngs-tools
Reusable tools for working with next-generation sequencing (NGS) data
biobenkj/QDNAseq_bin_annotations
This repo contains bin annotations for QDNAseq CNA calling
biobenkj/seqspec
biobenkj/sleuth
Differential analysis of RNA-Seq
biobenkj/spiky
biobenkj/stormseq_protocols
This repository contains the current STORM-seq protocol for library construction and analysis
biobenkj/synthbar
Add synthetic cell barcode to FASTQ reads
biobenkj/TE_expression_in_scRNAseq
biobenkj/vaigs_teaching
biobenkj/velocessor
velocity processor
biobenkj/WGBS_Biscuit_Snakemake
Snakemake Workflow For WGBS Data
biobenkj/wzmetagene
Create sub-intervals from intervals