bioThai

dockerc

container image to single executable compiler

slamseq

SLAMSeq processing and analysis pipeline

amethyst

An analysis toolkit for single-cell methylation sequencing data

sceasy

A package to help convert different single-cell data formats to each other

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity

scFEA

single cell Flux Estimation Analysis (scFEA) Try the below web server!

cloneRanger

MAPS

LARRY

cutTag-pipeline

Pipeline for Cut&Tag analysis

Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.

PENCIL

PENCIL is a novel tool for singlecell data analysis to identify phenotype associated subpopulations and informative genes simultaneously.

OpenCFU

An easy-to-use C++ application to count bacterial colonies (i.e. CFU).

ATAC-seq

Basic workflow for ATAC-seq analysis

deepStats

deepStats: a stastitical toolbox for deeptools and genomic signals

ArchRtoSignac

An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)

seqtk

Toolkit for processing sequences in FASTA/Q formats

EChO

Enhanced Chromatin Occupancy (EChO)

genemania

GeneMANIA helps you predict the function of your favourite genes and gene sets.

bwtool

A tool for bigWig files.

trackplot

Generate IGV style locus tracks from bigWig files in R

scATAC-seq_notes

scATAC-seq data analysis tools and papers

Bioinformatics_notes

Bioinformatics and genomics resources

dotfiles

Just my dotfiles setup, nothing fancy here.

unidex

python implementation of a universal demultiplexer built in mind for combinatorial indexing

excluderanges

Genomic coordinates of problematic genomic regions as GRanges

regulon-enrichment