LGGray

inactiveXX

Detect X-inactivation status in single cell transcriptomes

cellXY

R package to predict sex of single cells and identify Male/Female doublets using machine learning approaches

DRPT

plot1cell

ANANSE

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

MLmetrics

Machine Learning Evaluation Metrics

spASE

detecting spatial patterns of allele-specific expression

scHLAcount

Count HLA alleles in single-cell RNA-seq data

scarches

Reference mapping for single-cell genomics

DAseq

scFeatures

scib

Benchmarking analysis of data integration tools

Cytocipher

Analysis methods for analysing single cell RNA-seq data; particularly with the goal of checking if tentative clusters of cells are significantly different to one another in terms of their gene expression.

numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

scGENA

single cell Gene co-Expression Network Analysis

genomation

R package for genomic feature analysis and visualization

nichenetr

NicheNet: predict active ligand-target links between interacting cells

AAnet

Archetypal Analysis network (AAnet)

lionessR

Single sample network reconstruction in R

VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Cross-Entropy-test

Simplified script for applying the t-SNE diff method on high parameter flow cytometry data

CellphoneDB

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

iDEA

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

WASP

WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery

CloudPred

Predicting Individual Outcome From Heterogeneous Point Clouds

MetaNeighbor

CellChat

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

UCell

Gene set scoring for single-cell data

wesanderson

A Wes Anderson color palette for R

gchromVAR

Cell type specific enrichments using finemapped variants and quantitative epigenetic data