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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GENEPOP Resource Report Resource Website 1000+ mentions |
GENEPOP (RRID:SCR_009194) | Genepop | data analysis software, software resource, data processing software, software application | Population genetic data analysis software package. Used to perform exact Hardy Weinberg Equilibrium test. Used for population differentiation and for genotypic disequilibrium among pairs of loci. Computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc. and performs analyses of isolation by distance from pairwise comparisons of individuals or population samples., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Population, differentation, genetic, data, analysis, Hardy Weinberg Equilibrium test, statistics, genotyping, disequilibrium, pair, loci, allele, frequency |
is listed by: Genetic Analysis Software is listed by: CRAN |
PMID:21585727 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154337 | https://kimura.univ-montp2.fr/~rousset/Genepop.htm, https://cran.r-project.org/web/packages/genepop/index.html | SCR_009194 | genepop'007 | 2026-08-02 09:05:33 | 2266 | |||||
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Genetic Analysis Software Resource Report Resource Website 1+ mentions |
Genetic Analysis Software (RRID:SCR_013155) | GAS | catalog, software resource, data or information resource, database, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Listing of computer software for the gene mapping community on the following topics: genetic linkage analysis for human pedigree data, QTL analysis for animal/plant breeding data, genetic marker ordering, genetic association analysis, haplotype construction, pedigree drawing, and population genetics. The inclusion of a program should not be interpreted as an endorsement to that program from us. In the last few years, new technology produces new types of genetic data, and the scope of genetic analyses change dramatically. It is no longer obvious whether a program should be included or excluded from this list. Topics such as next-generation-sequencing (NGS), gene expression, genomics annotation, etc. can all be relevant to a genetic study, yet be specialized topics by themselves. Though programs on variance calling from NSG can be in, those can sequence alignment might be out; programs on eQTL can be in, those on differential expression might be out. This page was created by Dr. Wentian Li, when he was at Columbia University (1995-1996). It was later moved to Rockefeller University (1996-2002), and now takes its new home at North Shore LIJ Research Institute (2002-now). The present copy is maintained by Jurg Ott as a single file. More than 240 programs have been listed by December 2004, more than 350 programs by August 2005, close to 400 programs by December 2006, and close to 480 programs by November 2008, and over 600 programs by October 2012. A version of the searchable database was developed by Zhiliang Hu of Iowa State University, and a recent round of updating was assisted by Wei JIANG of Harbin Medical School. Some earlier software can be downloaded from EBI: ftp://ftp.ebi.ac.uk/pub/software/linkage_and_mapping/ (Linkage and Mapping Software Repository), and http://genamics.com/software/index.htm may contain archived copy of some programs. | gene mapping, gene, genetic, genomic, model, modeling, software program, genetic linkage analysis, qtl analysis, genetic marker order, genetic association analysis, haplotype construction, pedigree drawing, population genetics |
is used by: NIF Data Federation lists: EM-DECODER lists: ENTROPY BLOCKER lists: SOAP lists: ADEGENET lists: 2LD lists: SQTL lists: POLYMORPHISM lists: EDAC lists: FEST lists: GENEHUNTER SAD lists: COMDS lists: CHAPLIN lists: CRIMAP lists: DCHIP LINKAGE lists: FLOSS lists: HAP 1 lists: HAPSCOPE lists: LDB/LDB+ lists: LOCUSMAP lists: MRH lists: PEDIGREE-VISUALIZER lists: PEDPHASE lists: QTL CAFE lists: RHMAPPER lists: R/GC, R/GCF lists: R/GWAPOWER lists: R/WEIGHTED FDR lists: SIMM lists: SOLAR lists: TDTHAP lists: HWESTRATA lists: TDT-PC lists: EQTL EXPLORER lists: GAS2 lists: LDMET lists: LAMBDAA lists: EIGENSOFT/EIGENSTRAT lists: Happy lists: LAMP lists: CLUSTAG lists: OSA lists: SIMIBD lists: SNPSTATS lists: Haploview lists: QGene lists: PAWE-3D lists: MILD lists: PEDPLOT lists: GS-EM lists: PEDSCRIPT lists: Multipoint Identical-by-descent Method lists: PARENTE lists: Integrated Software lists: PEDRAW/WPEDRAW lists: POPDIST lists: TDTASP lists: TDTPOWER lists: TDT/S-TDT lists: HAPLOBLOCKFINDER lists: HAPMIXMAP lists: Genotype-IBD Sharing Test lists: LDGROUP lists: LDHAT lists: LDMAP lists: LDHEATMAP lists: LDSELECT lists: LINKAGE lists: LDSUPPORT lists: FASTLINK lists: LINKAGE - CEPH lists: LSP lists: Whap lists: TREESCAN lists: Graphical Overview of Linkage Disequilibrium lists: MAIA lists: MULTIMAP lists: R/ADEGENET lists: R/ENTROPY BLOCKER lists: BEAM lists: BMAPBUILDER lists: POPGEN lists: RTDT lists: R/SPECTRAL-GEM lists: R/STEPWISE lists: HAPLOCLUSTERS lists: TKMAP lists: CLUMP lists: FAMOZ lists: INTEGRAYEDMAP lists: SIBMED lists: POOLSCORE lists: LDA lists: LAPSTRUCT lists: BETA lists: ALTree lists: TRANSMIT lists: ETDT lists: R/TDTHAP lists: RVTESTS lists: S lists: ET-TDT lists: ILR lists: MAPCREATOR lists: MAPMAKER/SIBS lists: MAP MANAGER QT lists: MGA-MAPF2 lists: Pedigree-Draw lists: FASTMAP (1) lists: ASPEX lists: PEDJAVA lists: PEDPEEL lists: SIMCOAL lists: SNPHAP lists: SNPHARVESTER lists: SNP-HWE lists: TAGSNP lists: FASTMAP (2) lists: FASTSLINK lists: GASP lists: GENOGRAM-MAKER lists: GENEHUNTER++SAD lists: GENEPI.JAR lists: BDGEN lists: TLINKAGE lists: GENOME lists: EASYPOP lists: GENOMESIMLA lists: TRAP lists: CARTHAGENE lists: ACT lists: ADMIXMAP lists: 2DMAP lists: ALBERT lists: 2SNP lists: AGEINF lists: ALLASS lists: PEDIGREEQUERY lists: PATH lists: MULTIQTL lists: SPERMSEG lists: FASTER lists: Platypus lists: KIN lists: SNP ASSISTANT lists: GRONLOD lists: COMBIN lists: ARLEQUIN lists: SEGPATH lists: JENTI lists: SCOUT lists: HAPLOREC lists: UNPHASED lists: POWER lists: HAPLO 1 lists: HAPLO 2 lists: CHIP2SPELL lists: MAP MANAGER QTX lists: G-MENDEL lists: ASSOCIATIONVIEWER lists: WHICHRUN lists: GENECLASS lists: MAREYMAP lists: HELIXTREE lists: SVCC lists: GENEHUNTER-MODSCORE lists: FAMHAP lists: BAMA lists: WEBQTL lists: HAPLOVISUAL lists: CASPAR lists: GC/GCF lists: MIXSCORE lists: POWQ lists: QTLNetwork lists: SIMULAPLOT lists: SQTDT/SPDT lists: FESTA lists: BOTTLENECK lists: PAP lists: QUANTO lists: R/QTL lists: SNPEM lists: GENEPOOL lists: EPISTACY lists: VITESSE lists: LEA lists: DMAP lists: MOSCPHASER lists: UMAKE lists: TDT-AE lists: HAPLOWSER lists: STEPC lists: RECORD lists: QUTIE lists: R/COMPOSITELD lists: FINESSE lists: R/EHP lists: R/HCLUST lists: STEPWISE lists: genehunter-imprinting lists: PBAT lists: R/BARS lists: HARDY lists: R/ARP.GEE lists: R/COVIBD lists: STRAT lists: TREELD lists: TUNA lists: SIBSIM lists: IGG lists: ALLELIX lists: ALLEGRO lists: ALOHOMORA lists: ALP lists: AMELIA lists: ANALYZE lists: ANCESTRY lists: APE lists: BARS lists: APL-OSA lists: APM lists: ARIEL lists: GENOMIZER lists: ASP/ASPSHARE lists: BIMBAM lists: BIOIDE lists: BIOLAD-DB lists: BLADE lists: BLOCK lists: BOOLD lists: BOOSTRAPPER lists: BPPH lists: BQTL lists: DNABASER lists: Calculator for Association with Two Stage design lists: CC-QLS lists: CCRAVAT lists: CCREL lists: CEPH2CRI lists: CEPH2MAP lists: EVOKER lists: CFC lists: CHECKHET lists: MATLINK lists: CHECKMATRIX lists: CHIAMO lists: CHROMOSCAN lists: CHROMOSEG lists: COPE lists: HCLUST lists: COVIBD lists: CRIMAP-PVM lists: CROSSFIND lists: DGENE lists: EHPLUS lists: DHSMAP lists: DISENTANGLER lists: MAKEPED lists: DOLINK lists: DPPH lists: GREGOR lists: EAGLET lists: EASYLINKAGE/EASYLINKAGE-PLUS lists: EH lists: EHAP lists: EHP lists: EMLD lists: EPDT lists: ERPA lists: EXOMEPICKS lists: R/META lists: FASTEHPLUS lists: FASTLINK lists: FBAT lists: FINETTI lists: FIRSTORD lists: FISHER lists: GAIA lists: GAP lists: GAS lists: GCHAP lists: GDA lists: GEMS lists: GENECOUNTING lists: GENEFINDER lists: GENEHUNTER lists: GENEHUNTER-IMPRINTING lists: GENEHUNTER-PLUS lists: GENEPOP lists: GENERECON lists: GENESPRING GT lists: GENIE lists: GENETIC POWER CALCULATOR lists: GENETSIM lists: GENOOM lists: GENEVAR lists: GENEWEAVER lists: GENOCHECK lists: GENOPROOF lists: GENTOOLS lists: GEST lists: GEVALT lists: GGT lists: GHOST lists: GLIDERS lists: GLUE lists: GMA lists: GMCHECK lists: GSMA lists: GTOOL lists: GWAPOWER lists: HAP 2 lists: HAPAR lists: HAPASSOC lists: HAPBLOCK lists: HAPGEN lists: HAPINFERX lists: HAPLOBLOCK lists: HAPLOBUILD lists: HAPLOPOOL lists: HAPLORE lists: HAPLO.STAT lists: HAPLOT lists: HAPLOTTER lists: TWOLOC lists: HAPLOTYPE ESTIMATION lists: HAPLOTYPER lists: HAPMINER lists: HAP-SAMPLE lists: HAPSIMU lists: HIT lists: HOMOG/HOMOGM lists: HOTSPOTTER lists: HPLUS lists: HS-TDT lists: HTR lists: HTSNPER lists: MDR-PDT lists: INTERSNP lists: IMPUTE lists: NOPAR lists: JLIN lists: JOINMAP lists: JPSGCS lists: J/QTL lists: KING lists: LAMARC lists: LINKAGE-IMPRINT lists: LINKBASE lists: LIPED lists: LNKTOCRI lists: LOCUSZOOM lists: LOGINSERM ESTIHAPLO lists: LOH-LINKAGE lists: LOKI lists: LOT lists: L-POP lists: LRP lists: LRTAE lists: LTSOFT lists: MADMAPPER lists: Marker And Gene Interpolation and Correlation lists: MALDSOFT lists: MAMA lists: MANTEL-STRUCT lists: MAP/MAP+/MAP+H/MAP2000 lists: MAPCHART lists: MIDAS lists: MAPDISTO lists: MAPDRAW lists: MAPINSPECT lists: MAPL lists: MARGARITA lists: MDBLOCKS lists: MAPMAKER/EXP lists: MAPMAKER/HOMOZ lists: MAPMAKER/QTL lists: MAPQTL lists: MCQTL lists: MEGA2 lists: MEGASNPHUNTER lists: MENDEL lists: MERLIN lists: MFLINK lists: MINIMAC lists: MINSAGE lists: MITPENE lists: MKGST lists: MMDRAWER lists: MLBGH lists: MLD lists: MLR-TAGGING lists: PEDMANAGER lists: SAGE lists: MPDA lists: MULTIDISEQ lists: MULTIMAPPER lists: MULTIMAPPER/OUTBRED lists: MULTIPOPTAGSELECT lists: MULTISIM lists: MUTAGENESYS lists: NOCOM lists: NUCULAR lists: ONEMAP lists: OSIRIS lists: P ACT lists: PASS PEDIGREE lists: PAWE lists: PDA lists: PDPSYS lists: PDT lists: PED lists: PEDAGREE lists: PEDCHECK lists: PEDSTATS lists: PEDSYS lists: PEDVIZAPI lists: PEER lists: PHASE lists: PLABSIM lists: PL-EM lists: POINTER lists: POOL STR lists: POWERMARKER lists: POWERTRIM lists: POWTEST lists: PREPLINK lists: PREST lists: PROBMAX lists: PROC QTL lists: PROFILER lists: PRT lists: PSAT lists: SAS/GENETICS lists: PSEUDO lists: PSEUDOMARKER lists: PSEUDOMARKER.M lists: R/LDHEATMAP lists: QTL-ALL lists: QTL Cartographer lists: QTL EXPRESS lists: QU-GENE lists: RISCALW lists: RC-TDT lists: REAPER lists: RELATIVE lists: RELATIVEFINDER lists: RELCHECK lists: RELPAIR lists: RELTYPE lists: RHMAP lists: ROMPREV lists: ROSATTA SYLLEGO SYSTEM lists: R/GAP lists: R/HAPASSOC lists: R/IBDREG lists: R/LAPSTRUCT lists: R/LDGROUP lists: R/LUCA lists: R/METASIM lists: R/ONEMAP lists: R/PIAGE lists: R/POOLSCORE lists: R/POPGEN lists: R/QTLBIM lists: R/SNP.PLOTTER lists: SDMINP lists: SELSIM lists: SEQUENCE LD/SEQUENCE LDHOT lists: SIBERROR lists: SIBLINK lists: SIB-PAIR lists: SILCLOD lists: SIMLA lists: SNP CHART lists: SIMLINK lists: SIMPED lists: SIMPLE lists: SIMULA lists: SIMULATE lists: SIMUPOP lists: SIMWALK lists: START lists: SKAT lists: SLINK lists: SMOOTH lists: Suite of Nucleotide Analysis Programs lists: SNAP 3 lists: SNPALYZE lists: SNPFILE lists: SNPLINK lists: SNPP lists: SNP.PLOTTER lists: SNPTEST lists: SPAM lists: SPECTRAL-GEM lists: SPERM lists: SPIP lists: SPLAT lists: TAGSTER lists: SPLINK lists: SSAHASNP lists: SUMSTAT lists: SUP lists: SWEEP lists: TAGGER lists: TFPGA lists: TREESELECT lists: UNKNOWN lists: UTIL lists: WHAIT lists: ZAPLO lists: HAPBLOCK 2 lists: PLABQTL lists: TASSEL lists: MCLEEPS lists: SASGENE lists: PANGAEA lists: TOMCAT lists: SCORE-SEQ lists: SASQUANT lists: QMSIM lists: PIAGE lists: PEDPACK lists: INSEGT lists: IBDREG lists: GLFSINGLE/GLFTRIO/GLFMULTIPLES lists: GGSD lists: ECLIPSE lists: CHROMSCAN lists: COMPOSITELD lists: BOOST lists: ARP.GEE lists: BOREL lists: GASSOC lists: MENDELSOFT lists: PLINK/SEQ lists: POLYPHEN lists: SPREG lists: MOLKIN lists: PRESTO: Genetic Association Analysis Software lists: ENDOG lists: BEAGLECALL lists: GWASELECT lists: HEGESMA lists: SNIPPEEP lists: TAGIMPUTE lists: SNPMSTAT lists: SNP HITLINK lists: MECPM lists: R/FEST lists: MAOS lists: SUPERLINK lists: PEDFIDDLER lists: VG lists: HAPSTAT lists: QTDT lists: GRIDQTL lists: VH lists: R/QTLDESIGN lists: PyPop lists: ANTMAP lists: MDR lists: WEIGHTED FDR lists: THESIAS lists: DMLE lists: SGS lists: BAYESFST lists: HWMET lists: GRR lists: AUTOSCAN lists: TRIMHAP lists: ILLUMINUS lists: PELICAN lists: HAPLOPAINTER lists: HOMOZYGOSITYMAPPER lists: GERMLINE lists: PLINK lists: MACH 1.0 lists: BEAGLE lists: BIRDSUITE lists: BREAKDANCER lists: CAROL lists: CASAVA lists: CYRILLIC lists: DINDEL lists: GenABEL lists: GATK lists: PEDIGRAPH lists: MADELINE lists: METAL lists: OLORIN lists: PEDHUNTER lists: POLYMUTT lists: SAMTOOLS lists: SNAP - SNP Annotation and Proxy Search lists: STRUCTURE lists: SVA lists: SYZYGY lists: VAAST lists: Hapmix lists: Ancestrymap lists: Hmmer lists: PROGENY lists: VarScan lists: MORGAN lists: CMAP lists: SIMHAP lists: SIFT lists: ANNOVAR lists: Body Mass Index Calculator lists: PolyPhen: Polymorphism Phenotyping has parent organization: Feinstein Institute for Medical Research has parent organization: Iowa State University; Iowa; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33506 | http://lab.rockefeller.edu/ott/geneticsoftware | http://linkage.rockefeller.edu/soft/ | SCR_013155 | An Alphabetic List of Genetic Analysis Software | 2026-08-02 09:06:07 | 9 | |||||
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CRAN Resource Report Resource Website 5000+ mentions |
CRAN (RRID:SCR_003005) | CRAN | software resource, software repository | Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language. | network, ftp, web, server, code, documentation, mirror, R |
lists: lme4 lists: R package: nlme lists: R package: lmerTest lists: R package: RVAideMemoire lists: R package: LMERConvenienceFunctions lists: R package: psy lists: R package: lattice lists: geomorph lists: Sequenza lists: NeuroAnatomy Toolbox lists: dplyr lists: Prophet lists: metagear lists: tidyr lists: Mediation Analysis of Causality under Confounding lists: MIIVsem lists: rjags lists: GENEPOP lists: webchem lists: cowplot lists: readxl lists: biomod2 lists: multcomp lists: knitr lists: ggtree lists: Minimum-Hypergeometric Test lists: meta lists: Network-Based R-Statistics lists: pavo lists: Modern Applied Statistics with S lists: cvequality lists: openxlsx lists: tidyverse lists: Genomic Annotation in Livestock for positional candidate LOci lists: igraph lists: SIMR lists: gbs2ploidy lists: vioplot lists: spdep lists: maps lists: Differential Gene Correlation Analysis lists: ez lists: celltrackR lists: rentrez lists: pepr lists: survival lists: ggpubr lists: Signac lists: rstatix lists: ggalluvial lists: purrr lists: gtsummary lists: questionr lists: powereQTL lists: RSurveillance lists: epiR lists: psych lists: CCP lists: yacca lists: DHARMa lists: Companion to Applied Regression lists: Peptides lists: taxize lists: seqinr lists: reshape2 lists: mvabund lists: CpGassoc lists: metaMA lists: ComplexUpset lists: eulerr lists: shinyhelper lists: shinythemes lists: philentropy lists: lwgeom lists: stringr lists: ordinal lists: msigdbr lists: meta4diag lists: Rtrack lists: ggsignif lists: Corrplot lists: immunarch lists: Algorithms and Framework for Nonnegative Matrix Factorization lists: Computing Chance Corrected Agreement Coefficients lists: Intraclass Correlations for Quantifying Inter Rater Reliability lists: Regression Modeling Strategies lists: caret lists: AICcmodavg lists: RHRV lists: FFTrees lists: Simple Features lists: rworldmap lists: eHDprep lists: vcfR lists: vtree lists: SimplyAgree lists: randomizeR lists: DiagrammeR lists: forestplot lists: merTools lists: clusterSim lists: bibliometrix lists: Rtsne lists: brms lists: oncoPredict lists: epitools lists: DrugSim2DR lists: rstanarm lists: scCustomize lists: corrplot lists: Parsnip lists: ggbreak lists: FactoMineR lists: tidycmprsk lists: BioCircos lists: Matrix based Flexible Project Planning is affiliated with: R Project for Statistical Computing is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is affiliated with: ANOCVA is related to: flowBin is related to: CorMut is related to: VariantAnnotation is related to: timecourse is related to: RmiR.Hs.miRNA is related to: PSCBS is related to: sybil - Efficient Constrained Based Modelling in R is related to: categoryCompare is related to: clValid is related to: pheatmap is related to: RaceID is related to: BRASS is related to: IDR is related to: ascend is related to: brainGraph is related to: GBM R package is related to: Phangorn is related to: ape is related to: missForest is related to: trend is related to: precrec is related to: EHRtemporalVariability is related to: emmeans is related to: reshape is related to: variancePartition is related to: SimFFPE is related to: FilterFFPE is related to: shinyCircoss is related to: Betareg is related to: ggeffects is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: ggforce is related to: janitor is related to: Rphenograph is parent organization of: Postgwas is parent organization of: MetaDE is parent organization of: MCMC.qpcr is parent organization of: PurBayes is parent organization of: circlize is parent organization of: neuRosim is parent organization of: metaRNASeq is parent organization of: RankAggreg is parent organization of: DEMI is parent organization of: Iterative Signature Algorithm is parent organization of: MUMA is parent organization of: VennDiagram is parent organization of: ExomeDepth is parent organization of: FisHiCal is parent organization of: CNVassoc is parent organization of: aCGH.Spline is parent organization of: Isopat is parent organization of: enviPat is parent organization of: Parametric Time Warping is parent organization of: enviPick is parent organization of: pairheatmap is parent organization of: RCircos is parent organization of: MultiPhen is parent organization of: aLFQ is parent organization of: MetaQC is parent organization of: YuGene is parent organization of: Kdetrees is parent organization of: ggplot2 is parent organization of: R package inTrees is parent organization of: ggrepel hosts: MSM |
nif-0000-30270 | http://cran.r-project.org/mirrors.html | SCR_003005 | the Comprehensive R Archive Network, Comprehensive R Archive Network, The Comprehensive R Archive Network | 2026-08-02 09:03:31 | 5947 |
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