Alternatives and similar repositories for plink-ng

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

• YinLiLin / CMplot
  📊 Circular and Rectangular Manhattan Plot
  ☆583Updated 4 months ago
• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆470Updated last month
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆305Updated 2 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆448Updated last year
• 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.
  ☆535Updated 2 months ago
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆331Updated 2 months ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆429Updated this week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆392Updated last week
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆498Updated last week
• rgcgithub / regenie
  regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
  ☆223Updated 2 months ago
• cooplab / popgen-notes
  Population genetics notes
  ☆673Updated 2 years ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆404Updated 2 weeks ago
• DReichLab / EIG
  Eigen tools by Nick Patterson and Alkes Price lab
  ☆188Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆376Updated 2 months ago
• choishingwan / PRSice
  A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
  ☆199Updated 11 months ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆693Updated 4 months ago
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆335Updated 2 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆508Updated last week
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆520Updated last year
• knausb / vcfR
  Tools to work with variant call format files
  ☆260Updated 5 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• bulik / ldsc
  LD Score Regression (LDSC)
  ☆721Updated 11 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆438Updated last year
• genetics-statistics / GEMMA
  Genome-wide Efficient Mixed Model Association
  ☆366Updated last month
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆192Updated 3 years ago
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆839Updated 2 months ago
• xiaolei-lab / rMVP
  A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
  ☆305Updated 3 weeks ago
• hbctraining / DGE_workshop
  ☆392Updated 3 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆753Updated last week