candacechan

tdigest

t-Digest data structure in Python. Useful for percentiles and quantiles, including distributed enviroments like PySpark

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

gggenomes

A grammar of graphics for comparative genomics

complex-upset

A library for creating complex UpSet plots with ggplot2 geoms

bioinfokit

Bioinformatics data analysis and visualization toolkit

plotgardener

ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

AGEpy

Bioinformatics tools for Python

pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks

textdistance

📐 Compute distance between sequences. 30+ algorithms, pure python implementation, common interface, optional external libs usage.

hicGAN

Hi-C data super-resolution with generative adversarial networks

multipy

Multiple hypothesis testing in Python

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

ggbreak

:broken_heart: An implementation of scale functions for setting axis breaks of a 'gg' plot.

genewalk

GeneWalk identifies relevant gene functions for a biological context using network representation learning

SegLossOdyssey

A collection of loss functions for medical image segmentation

unet

unet for image segmentation

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

Toucan

sync, backup and secure, all in one place

gdrive

Google Drive CLI Client

ataqv

A toolkit for QC and visualization of ATAC-seq results.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.