fenglin0 / benchmarking_variant_callers
In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We evaluate the performances of these tools in different read depths, genomic contexts,…
☆15Updated 5 years ago
Alternatives and similar repositories for benchmarking_variant_callers:
Users that are interested in benchmarking_variant_callers are comparing it to the libraries listed below
- Analyzing chromatin accessibility data in R☆18Updated last year
- ☆12Updated 3 years ago
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆19Updated last year
- ☆12Updated 5 years ago
- Snakemake pipeline for plate scATAC-seq processing☆26Updated last year
- Analysis cell-type-specific functional gene network, with SCINET and HumanNetv3☆39Updated last year
- Data analysis pipeline for scNT-seq (single-cell metabolically labeled new RNA tagging sequencing)☆16Updated last year
- Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation☆21Updated 8 months ago
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆19Updated 2 years ago
- Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"☆10Updated 5 years ago
- Bead-based single-cell atac processing☆31Updated 3 years ago
- Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.☆14Updated 2 years ago
- Gene Expression Decomposition and Integration☆17Updated 3 weeks ago
- ☆16Updated 2 years ago
- Code associated with MIX-seq manuscript☆14Updated 4 years ago
- ☆45Updated 7 months ago
- scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper☆23Updated 2 years ago
- ☆16Updated 9 months ago
- ☆20Updated last year
- ☆32Updated 10 months ago
- MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-s…☆20Updated 3 months ago
- Advanced steps of the OSCA book☆12Updated this week
- ☆17Updated 4 years ago
- Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression☆15Updated 8 months ago
- An end-to-end computational pipeline for large Perturb-seq screens☆13Updated 2 years ago
- Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq☆16Updated 3 weeks ago
- epigenome analysis to rank transcription factors☆13Updated 5 years ago
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆36Updated last week
- software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data☆17Updated 5 years ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆31Updated last year