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 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
Sorting:
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆20Updated 3 years ago
- ☆12Updated 4 years ago
- scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper☆24Updated 2 years ago
- Snakemake pipeline for plate scATAC-seq processing☆26Updated last year
- ☆22Updated last year
- Analyzing chromatin accessibility data in R☆18Updated 2 years ago
- ☆18Updated 4 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 2 years ago
- Data analysis pipeline for scNT-seq (single-cell metabolically labeled new RNA tagging sequencing)☆16Updated 2 years ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆33Updated 5 months ago
- Bead-based single-cell atac processing☆33Updated 3 years ago
- Gene Set + S2G strategy annotations analyzed for disease architecture☆54Updated 2 years ago
- ☆17Updated 2 years ago
- Publication Page for the Noack et al. 2021 Nature Neuroscience paper☆10Updated 3 years ago
- Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis☆34Updated 3 years ago
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆41Updated 2 years ago
- Tool for modelling of mitochondrial heteroplasmy☆18Updated last year
- ☆19Updated 2 years ago
- ☆20Updated 2 years ago
- Codes for our paper "Single-Cell RNA-Seq Reveals Dynamic Early Embryonic-like Programs during Chemical Reprogramming" published by Cell S…☆11Updated 5 years ago
- ☆25Updated last year
- scover☆23Updated last year
- ☆22Updated 4 years ago
- <<------ Use SnapATAC!!☆25Updated 6 years ago
- ☆16Updated 2 years ago
- ☆16Updated 2 years ago
- ☆12Updated 6 years ago
- STAR, cufflinks, cluster, DESeq2, GO analysis☆14Updated 5 years ago
- ☆51Updated last year
- Repo for website and other code for mouse sci-ATAC-seq project☆28Updated 4 years ago