fenglin0 / benchmarking_variant_callersLinks
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,…
☆16Updated 6 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
Sorting:
- Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis☆35Updated 4 years ago
- Data analysis pipeline for scNT-seq (single-cell metabolically labeled new RNA tagging sequencing)☆16Updated 2 years ago
- ☆20Updated 2 years ago
- scover☆24Updated 2 years ago
- ☆20Updated 5 years ago
- A method which leverages scRNA-seq data to achieve two goals: (1) to infer the cell types in which the disease-associated genes manifest …☆26Updated 3 years ago
- scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper☆25Updated 3 years ago
- ☆19Updated 2 years ago
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆22Updated 3 years ago
- Snakemake pipeline for plate scATAC-seq processing☆26Updated 2 years ago
- ☆12Updated 4 years ago
- ☆19Updated 2 years ago
- Analyzing chromatin accessibility data in R☆18Updated 2 years ago
- Bead-based single-cell atac processing☆33Updated 4 years ago
- ScisorWiz: Differential Isoform Visualizer for Long-Read RNA Sequencing Data☆20Updated last year
- ☆53Updated last year
- software for analysis of chromatin feature occupancy profiles from high-throughput sequencing data☆17Updated 6 years ago
- ☆12Updated 4 years ago
- Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data☆27Updated 5 years ago
- Advanced steps of the OSCA book☆14Updated 2 months ago
- ☆25Updated 3 years ago
- ☆18Updated 2 years ago
- Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression☆15Updated last year
- Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)☆15Updated 5 years ago
- SCASA: Single cell transcript quantification tool☆22Updated 2 years ago
- Repo for website and other code for mouse sci-ATAC-seq project☆29Updated 5 years ago
- Analysis repository for "Droplet-based combinatorial indexing for massive scale single-cell epigenomics"☆11Updated 6 years ago
- ☆12Updated 4 years ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆32Updated 10 months ago
- Analysis pipeline for our circSC manuscript☆14Updated 3 years ago