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The Top 23 R Sequencing Open Source Projects

Open source projects categorized as R Sequencing
Adam ⭐ 966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 4 months ago
Phyloseq ⭐ 520
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
most recent commit 7 months ago
Snapatac ⭐ 227
Analysis Pipeline for Single Cell ATAC-seq
most recent commit 2 years ago
Smudgeplot ⭐ 200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
most recent commit 4 months ago
Splatter ⭐ 195
Simple simulation of single-cell RNA sequencing data
most recent commit 6 months ago
Minion_qc ⭐ 174
Quality control for MinION sequencing data
most recent commit 2 years ago
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 5most recent commit a year ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 years ago
Ngstools ⭐ 142
Programs to analyse NGS data for population genetics purposes
most recent commit 9 months ago
Rnaseq Workflow ⭐ 133
A repository for setting up a RNAseq workflow
most recent commit 7 years ago
Decontam ⭐ 122
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
most recent commit a year ago
Facets ⭐ 119
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
most recent commit a year ago
Purecn ⭐ 114
Copy number calling and variant classification using targeted short read sequencing
most recent commit 4 months ago
Ancombc ⭐ 87
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
most recent commit 4 months ago
Clonevol ⭐ 87
Inferring and visualizing clonal evolution in multi-sample cancer sequencing
most recent commit 4 years ago
Basics ⭐ 81
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
most recent commit 4 months ago
Ichorcna ⭐ 73
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
most recent commit 4 years ago
Stitch ⭐ 67
STITCH - Sequencing To Imputation Through Constructing Haplotypes
most recent commit 8 months ago
Canopy ⭐ 55
Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.
total releases 4most recent commit 3 years ago
Tenx ⭐ 53
Pipelines for the analysis of 10x single-cell RNA-sequencing data
most recent commit 10 months ago
Cnview ⭐ 50
Visualization and annotation of CNVs from population-scale whole-genome sequencing data
most recent commit 6 years ago
Dmrseq ⭐ 47
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
most recent commit 2 years ago
Rna Seq Diff Exprn ⭐ 44
RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).
most recent commit 11 years ago
The 2 Most Depended On R Sequencing Open Source Projects
Ngstk ⭐ 15
A toolkit developed by JhuangLab members to facilitate the analysis of next-generation sequencing (NGS) data.
dependent packages 1total releases 5latest release November 22, 2018most recent commit 5 years ago
The 7 Latest Releases In R Sequencing Open Source Projects
Sccatch ⭐ 171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
total releases 5latest release April 23, 2023most recent commit a year ago
Mapdamage ⭐ 37
mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
total releases 1latest release June 18, 2021most recent commit 8 months ago
Ctdnatools ⭐ 17
R package to work with ctDNA sequencing data
total releases 1latest release March 04, 2020most recent commit 2 years ago
Ngstk ⭐ 15
A toolkit developed by JhuangLab members to facilitate the analysis of next-generation sequencing (NGS) data.
dependent packages 1total releases 5latest release November 22, 2018most recent commit 5 years ago
Neutralitytestr ⭐ 8
Testing a neutral evolution model on cancer sequencing data
total releases 2latest release May 21, 2018most recent commit 3 years ago
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