Alternatives and similar repositories for GAPIT

Users that are interested in GAPIT are comparing it to the libraries listed below

• BGI-shenzhen / PopLDdecay
  PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
  ☆200Updated last year
• BGI-shenzhen / LDBlockShow
  LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
  ☆194Updated 5 months ago
• edgardomortiz / vcf2phylip
  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
  ☆323Updated 2 years ago
• TickingClock1992 / RIdeogram
  ☆189Updated 5 years ago
• xiaolei-lab / rMVP
  A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study
  ☆315Updated 2 months ago
• showteeth / ggcoverage
  Visualize and annotate genomic coverage with ggplot2
  ☆270Updated 10 months ago
• YuLab-SMU / MicrobiotaProcess
  A comprehensive R package for deep mining microbiome
  ☆190Updated last month
• TongZhou2017 / itol.toolkit
  Helper Functions for Interactive Tree Of Life (iTOL)
  ☆179Updated last month
• cafferychen777 / ggpicrust2
  Make Picrust2 Output Analysis and Visualization Easier
  ☆170Updated last month
• knausb / vcfR
  Tools to work with variant call format files
  ☆264Updated last month
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆122Updated last year
• bernatgel / karyoploteR
  karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
  ☆348Updated 6 months ago
• cxli233 / SimpleTidy_GeneCoEx
  A simple gene co-expression analyses workflow powered by tidyverse and graph analyses
  ☆212Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆216Updated last year
• YaoLab-Bioinfo / shinyCircos
  an R/shiny application for creation of Circos plot interactively
  ☆158Updated 3 years ago
• yiluheihei / microbiomeMarker
  R package for microbiome biomarker discovery
  ☆192Updated 9 months ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆148Updated 10 years ago
• ANGSD / angsd
  Program for analysing NGS data.
  ☆249Updated 9 months ago
• hahnlab / CAFE
  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
  ☆118Updated 4 years ago
• lh3 / psmc
  Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
  ☆178Updated 3 weeks ago
• YongxinLiu / Metagenome
  Metagenome analysis pipeline
  ☆99Updated 4 years ago
• JoniColeman / gwas_scripts
  Codebook from my GWAS cookbook
  ☆193Updated 3 years ago
• taowenmicro / ggClusterNet
  Microbial ecological network visualization clustering
  ☆133Updated 3 weeks ago
• YongxinLiu / Note
  ☆125Updated 4 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆227Updated 5 months ago
• mmatschiner / tutorials
  Tutorials on phylogenetic and phylogenomic inference
  ☆393Updated 2 years ago
• ewels / sra-explorer
  Web application to explore the Sequence Read Archive.
  ☆218Updated 4 months ago
• simonhmartin / genomics_general
  General tools for genomic analyses.
  ☆380Updated 9 months ago
• YongxinLiu / EasyMicrobiome
  ☆133Updated 2 weeks ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆270Updated 2 months ago