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:
- Snakemake pipeline for plate scATAC-seq processing☆26Updated last year
- single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition☆19Updated 2 years ago
- ☆18Updated 4 years ago
- Publication Page for the Noack et al. 2021 Nature Neuroscience paper☆10Updated 3 years ago
- Repo for generating custom blacklist for reads originating from mitochondrial DNA to nuclear genome☆20Updated 3 years ago
- Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis☆34Updated 3 years ago
- ☆17Updated 2 years ago
- Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles☆33Updated 6 months ago
- scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper☆24Updated 2 years ago
- ☆51Updated last year
- ☆12Updated 4 years ago
- Gene Set + S2G strategy annotations analyzed for disease architecture☆55Updated 2 years ago
- ☆23Updated last year
- ☆20Updated 2 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
- SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data☆41Updated 2 years ago
- Analysis code for "Perturbation-response genes reveal signaling footprints in cancer gene expression"☆20Updated 7 years ago
- Analytical tools and pipelines for bulk and single cell epigenomic and human genetic data☆27Updated 4 years ago
- ☆38Updated last month
- Toolkit for single-cell analysis of chromatin accessibility☆12Updated 5 years ago
- Analyzing chromatin accessibility data in R☆18Updated 2 years ago
- MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-s…☆20Updated 10 months ago
- Advanced steps of the OSCA book☆13Updated 5 months ago
- scover☆23Updated last year
- https://molecular-neurogenetics.github.io/truster/☆11Updated 2 months ago
- Code to reproduce analyses in Nasser, Bergman, Fulco, Guckelberger, Doughty et al Nature 2021☆15Updated 4 years ago
- Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression☆15Updated last year
- scGRO-seq analyses codes☆13Updated last year
- ☆25Updated 2 years ago
- TF analysis from epigenetic and Hi-C data☆18Updated 6 months ago