HoneyBADGER

Genetic variation detector

An R package that uses Bayesian inference and hidden Markov models to detect genetic variations in single-cell RNA-seq data

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

GitHub

96 stars
8 watching
31 forks
Language: R
last commit: over 3 years ago
Linked from 1 awesome list

bayesianbioinformaticscnv-detectionheterogeneityhmmsingle-cell-analysissingle-cell-rna-seqsubpopulationtranscriptomics

Backlinks from these awesome lists:

Related projects:

Repository Description Stars
nlawlor/v-sva An interactive R application to detect and annotate hidden sources of variation in single cell RNA-seq data 7
broadinstitute/infercnv Software to detect copy number variations from single-cell RNA-seq data using probabilistic modeling and machine learning algorithms 565
ncsa/genomicscortextvarnextflow A Nextflow-based pipeline for detecting structural variants in whole-genome reads using the Cortex-Var algorithm. 2
zeeev/wham Software tool for detecting and analyzing structural variants in genomes 103
brwnj/smoove-nf An automation workflow for detecting structural variations in genomic data using the smoove toolset 12
cortes-ciriano-lab/scomatic A tool for detecting somatic variants in single-cell data 170
ucarlab/iasva An R package that identifies hidden factors in data to uncover sources of variation 8
chris-mcginnis-ucsf/doubletfinder Detects doublets in single-cell RNA sequencing data by analyzing cell distances and proportions of artificial neighbors 415
nf-core/sarek Automated workflow for detecting germline or somatic variants in genomic sequencing data 409
edward130603/bayesspace A Bayesian model for clustering and enhancing spatial gene expression data 111
metagenomics/meragene An open-source software pipeline that uses Hidden-Markov-Models to identify genes in metagenomics data and provide reliable results 4
pachterlab/cwgflhgcchap_2021 Analyzing multiplexed single-cell RNA-seq data from a marine organism, providing tools for preprocessing, clustering, and analysis of gene expression across different cell types. 2
iarcbioinfo/needlestack An ultra-sensitive multi-sample variant caller for NGS data 49
josemarcosrf/hog-pedestrian-detector An implementation of a basic HOG + SVM pedestrian detector in MATLAB. 49
sridnona/cb_sniffer A tool that identifies and annotates genetic variants in single-cell RNA sequencing data by matching mutant and reference barcodes. 43