Alternatives and similar repositories for plink-ng:

Users that are interested in plink-ng are comparing it to the libraries listed below

• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆406Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆427Updated 11 months ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆467Updated this week
• YinLiLin / CMplot
  📊 Circular and Rectangular Manhattan Plot
  ☆549Updated 8 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆380Updated 2 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆357Updated 3 weeks ago
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆306Updated last year
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆411Updated last month
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆703Updated 3 weeks ago
• Cloufield / GWASTutorial
  GWAS Tutorial for Beginners
  ☆225Updated last month
• xiaolei-lab / rMVP
  A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
  ☆287Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆803Updated this week
• vcftools / vcftools
  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
  ☆517Updated last year
• weizhouUMICH / SAIGE
  ☆193Updated 2 years ago
• cole-trapnell-lab / cufflinks
  ☆314Updated 4 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆335Updated 6 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆720Updated this week
• thackl / gggenomes
  A grammar of graphics for comparative genomics
  ☆645Updated 2 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆491Updated this week
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆483Updated this week
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆487Updated 2 weeks ago
• rgcgithub / regenie
  regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
  ☆202Updated 3 weeks ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆457Updated last month
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆692Updated 2 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆370Updated 2 weeks ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆238Updated 2 years ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆632Updated 2 months ago
• DReichLab / EIG
  Eigen tools by Nick Patterson and Alkes Price lab
  ☆183Updated last year
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆190Updated 2 years ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆390Updated 5 months ago