biobenkj

dREG

Detecting Regulatory Elements using GRO-seq and PRO-seq

datathin

countsplit

espresso

Human-Bone-Marrow-Titration-Atlas

An Immunophenotypic and Transcriptomic Human Bone Marrow Atlas

FLASH-Seq

gtfsort

A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm.

cellstates

Finding gene expression states in scRNA-seq data

NASC-seq2

ceas

Cellular Energetics Analysis Software

telescope_annotation_db

Transposable element databases

telescope

Quantification of transposable element expression using RNA-seq

python-newick

python package to read and write the Newick format

demultiplex

Versatile FASTA/FASTQ demultiplexer.

fastq_demux

Demultiplex Illumina FASTQ files

BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

VASAseq

Collections of scripts used to map and analyze VASAseq data

synthbar

Add synthetic cell barcode to FASTQ reads

pyTSOfilter

python script to filter TSO artifact reads from aligned bam files

The-Art-of-Linear-Algebra

Graphic notes on Gilbert Strang's "Linear Algebra for Everyone"

VASAseq_2022

This repository aims to serve as an index of the work described at Salmen & De Jonghe et. al 2022

book

R for Mass Spectrometry documentation

fqme

modbam2bed

MultiAssayExperiments.jl

Julia implementation of Bioconductor's MultiAssayExperiment.

HDF5Arrays.jl

Julia implementation of Bioconductor's HDF5Array class.

GenomicFeatureVectors.jl

Julia implementation of Bioconductor's GenomicRanges(List) infrastructure.

SummarizedExperiments.jl

Julia implementation of Bioconductor's SummarizedExperiment class

JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

machine-learning-book

Code Repository for Machine Learning with PyTorch and Scikit-Learn