R package for analyzing single-cell RNA-seq data

Multi-sample somatic variant caller

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

R package to work with ctDNA sequencing data

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

This RNAseq data analysis tutorial is created for educational purpose

An R package to process and analyze transcriptomic data

RNA-seq, QC and differential analysis pipeline

Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Conta is an R package to detect cross contamination and source of contamination

A flexible, automation and pragmatic workflow tool to process the NGS data.

Population Genomics Pipeline used for SNPs data from VCF files.

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

CNV detection for prokaryote genomes using NGS sequencing data

Some very useful records for me.

SCORE - a consensus tool for detecting differentially expressed genes in bacteria

Framework to benchmark germline copy-number variant detection tools from NGS data

A QC pipeline for SVs calls based on coverage and SNP calls

AluScanCNV2 is an R package that integrates the cross-platform CNV detection and tumor prediction function on the basis of AluScanCNV software developed in the early stage.