JosephWayman

sc-SHC

Significance analysis for clustering single-cell RNA-sequencing data

BPCells

Scaling Single Cell Analysis to Millions of Cells

NetREX_CF

nichenetr

NicheNet: predict active ligand-target links between interacting cells

InteractiveComplexHeatmap

Make Interactive Complex Heatmaps

CSBB-Shiny

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

scriabin

Analysis of cell-cell communication at single-cell resolution

scarches

Reference mapping for single-cell genomics

r_tips

A repository of R usage tips for data cleaning, data mining, data visualisation, statistical inference and machine learning

maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

CellMixS

A cellspecific mixing score to evaluate group-/batch-specific bias in scRNA seq datasets

ComplexHeatmap

Make Complex Heatmaps

BiologicalProcessActivity

ELeFHAnt

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR

tidyheatmaps

Heatmaps from Tidy Data

ArchR

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

netSmooth

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

covid_balf

R script for the covid balf data analysis

ganspace

Discovering Interpretable GAN Controls [NeurIPS 2020]

awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

wesanderson

A Wes Anderson color palette for R

tabula-muris-senis

Tabula Muris Senis

baseline

Reproducible workflows for the data analysis of "Baseline" project

chromVARmotifs

R package with motifs for use with chromVAR

chromVAR

chromatin Variability Across Regions (of the genome!)

NetProphet_2.0

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Dual_Threshold_Optimization

Dual threshold optimization for identifying convergent evidence: TF binding locations and TF perturbation responses.

TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

cutadapt

Cutadapt removes adapter sequences from sequencing reads