Alternatives and similar repositories for plink-ng

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

• PoisonAlien / maftools
  Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
  ☆477Updated 3 months ago
• pachterlab / sleuth
  Differential analysis of RNA-Seq
  ☆306Updated 4 months ago
• YinLiLin / CMplot
  📊 Circular and Rectangular Manhattan Plot
  ☆593Updated 6 months ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆400Updated 2 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆416Updated last month
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆433Updated 2 months ago
• Ensembl / ensembl-vep
  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
  ☆506Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• DReichLab / EIG
  Eigen tools by Nick Patterson and Alkes Price lab
  ☆191Updated last year
• rgcgithub / regenie
  regenie is a C++ program for whole genome regression modelling of large genome-wide association studies.
  ☆232Updated last week
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆342Updated 4 months ago
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆384Updated 3 weeks ago
• choishingwan / PRSice
  A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
  ☆199Updated last year
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆702Updated 6 months ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated 2 months ago
• cooplab / popgen-notes
  Population genetics notes
  ☆675Updated 2 years ago
• samtools / bcftools
  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.gith…
  ☆812Updated 2 weeks ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆512Updated last month
• hbctraining / Training-modules
  Materials for short, half-day workshops
  ☆338Updated 3 weeks ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆737Updated 2 months ago
• cole-trapnell-lab / cufflinks
  ☆318Updated 5 years ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆524Updated last month
• hbctraining / DGE_workshop
  ☆400Updated 3 years ago
• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆414Updated this week
• shenlab-sinai / ngsplot
  Quick mining and visualization of NGS data by integrating genomic databases
  ☆266Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆259Updated 2 years ago
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆346Updated last month
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆541Updated last 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.
  ☆537Updated 4 months ago