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
98 stars
8 watching
31 forks
Language: R
last commit: about 5 years agoLinked from 1 awesome list
bayesianbioinformaticscnv-detectionheterogeneityhmmsingle-cell-analysissingle-cell-rna-seqsubpopulationtranscriptomics
seandavi/awesome-single-cellRelated 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 | 579 |
 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 | 104 |
 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 | 177 |
 ucarlab/iasva | Analyzes correlated hidden factors from single-cell transcriptomes to identify biological variation | 8 |
 chris-mcginnis-ucsf/doubletfinder | Detects doublets in single-cell RNA sequencing data by analyzing cell distances and proportions of artificial neighbors | 424 |
 nf-core/sarek | A workflow designed to detect germline and somatic variants from WGS and targeted sequencing data using bioinformatics tools. | 412 |
 edward130603/bayesspace | A Bayesian model for clustering and enhancing spatial gene expression data | 114 |
 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 | 50 |
 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. | 44 |