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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BAYESFST Resource Report Resource Website 1+ mentions |
BAYESFST (RRID:SCR_013479) | software application, software resource | Software application for Bayesian estimation of the coancestry coefficient FST (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154236, biotools:bayesfst | https://bio.tools/bayesfst | SCR_013479 | 2026-09-19 12:58:10 | 2 | |||||||||
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SUPERLINK Resource Report Resource Website 10+ mentions |
SUPERLINK (RRID:SCR_013360) | SUPERLINK | software application, software resource | Software program that performs exact linkage analysis with the same input-output relationships as in standard genetic linkage programs such as LINKAGE, FASTLINK, VITESSE, but can run larger files than previous programs. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, ms-windows, linux, macos x | is listed by: Genetic Analysis Software | nlx_154665 | SCR_013360 | 2026-09-19 12:58:09 | 23 | |||||||||
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HWMET Resource Report Resource Website |
HWMET (RRID:SCR_013480) | HWMET | software application, software resource | Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154404 | SCR_013480 | 2026-09-19 12:58:10 | 0 | |||||||||
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VH Resource Report Resource Website |
VH (RRID:SCR_013402) | VH | software application, software resource | Software application for displaying estimated haplotype data (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154689 | SCR_013402 | visual haplotype | 2026-09-19 12:58:10 | 0 | ||||||||
|
ECLIPSE Resource Report Resource Website 100+ mentions |
ECLIPSE (RRID:SCR_013130) | software application, software resource | A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, tested on, unix, (compaq tru64 v5.0a), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:eclipse, nlx_154290 | https://bio.tools/eclipse | SCR_013130 | Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA | 2026-09-19 12:58:09 | 124 | ||||||||
|
GRR Resource Report Resource Website |
GRR (RRID:SCR_013496) | GRR | software application, software resource | A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows | is listed by: Genetic Analysis Software | nlx_154365 | SCR_013496 | Graphical Representation of Relationships | 2026-09-19 12:58:10 | 0 | ||||||||
|
PEDFIDDLER Resource Report Resource Website |
PEDFIDDLER (RRID:SCR_013376) | PEDFIDDLER | software application, software resource | Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, c++, unix, (osf1, and solaris 2.7, alphalinux), ms-windows, (xp home/win32/win95), linux | is listed by: Genetic Analysis Software | nlx_154517 | SCR_013376 | PEDPACK in PANGAEA | 2026-09-19 12:58:09 | 0 | ||||||||
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VG Resource Report Resource Website 1+ mentions |
VG (RRID:SCR_013378) | VG | software application, software resource | Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154688 | SCR_013378 | Visual Genotype | 2026-09-19 12:58:10 | 3 | ||||||||
|
TAGIMPUTE Resource Report Resource Website |
TAGIMPUTE (RRID:SCR_013338) | software application, software resource | A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154670 | SCR_013338 | TAGging-snp based IMPUTATE | 2026-09-19 12:58:09 | 0 | |||||||||
|
SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software application, software resource | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-09-19 12:58:09 | 0 | |||||||
|
SGS Resource Report Resource Website |
SGS (RRID:SCR_013460) | SGS | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, visualbasic, ms-windows, (95/98/00/nt) | is listed by: Genetic Analysis Software | nlx_154054 | SCR_013460 | 2026-09-19 12:58:10 | 0 | |||||||||
|
AUTOSCAN Resource Report Resource Website 10+ mentions |
AUTOSCAN (RRID:SCR_013510) | AUTOSCAN | software application, software resource | A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software) | gene, genetic, genomic, c and unix-shell (bourne), unix, (solaris/dec-unix) | is listed by: Genetic Analysis Software | nlx_154235 | SCR_013510 | 2026-09-19 12:58:10 | 20 | |||||||||
|
eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-19 12:58:14 | 6 | ||||
|
CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-19 12:58:15 | 1908 | ||||||
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Mutant Mouse Resource and Research Center - Jackson Laboratory Resource Report Resource Website 10+ mentions |
Mutant Mouse Resource and Research Center - Jackson Laboratory (RRID:SCR_016446) | MMRRC JAX, JAX MMRRC, JAX MMR | biomaterial supply resource, material resource | Center for mutant mouse research and distribution. The objectives of the JAX MMRRC are to: identify and evaluate biomedically-significant mice, import/acquire and archive mouse strains, distribute mouse strains, and operate a control program to ensure genetic stability. | mouse, mutation, clinical, research, biomedicine, genetics, gene, strain | is organization facet of: Mutant Mouse Resource and Research Center | NIH Office of the Director U42 OD010921 | SCR_016446 | JAX Mutant Mouse Resource and Research Center, Mutant Mouse Resource and Research Center - JAX, Jackson Laboratory MMRRC, Jackson Laboratory Mutant Mouse Resource and Research Center | 2026-09-19 12:58:15 | 23 | ||||||||
|
SCENIC Resource Report Resource Website 100+ mentions |
SCENIC (RRID:SCR_017247) | data processing software, software application, software resource | Software R package as single cell regulatory network inference and clustering. Used for simultaneous gene regulatory network reconstruction and cell state identification from single cell RNA-seq data. | single, cell, regulatory, network, inference, clustering, simultaneous, gene, reconstruction, single, RNA-seq, data | ERC Consolidator Grant ; Foundation Against Cancer ; Special Research Fund (BOF) KU Leuven ; The Research Foundation - Flanders |
PMID:28991892 | Free, Available for download, Freely available | https://aertslab.org/#scenic | SCR_017247 | 2026-09-19 12:56:07 | 161 | ||||||||
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Primer Express Software Resource Report Resource Website 1+ mentions |
Primer Express Software (RRID:SCR_017376) | data analytics software, data processing software, software application, software resource | Software tool by Applied Biosystems to design primers and probes using TaqMan and SYBR Green I dye chemistries for gene quantitation and allelic discrimination (SNP) real-time PCR applications. Developed for use with StepOne, StepOnePlus, 7300, 7500, 7500 Fast, 7900HT, ViiA 7, and QuantStudio real-time PCR systems. Provides customized application specific documents for absolute⁄relative quantitation and allelic discrimination. | Applied Biosystems, ThermoFisher Scientific, design, primer, probe, TaqMan, SYBR Green, gene, quantitation, allelic, discrimination, RT PCR | Restricted | SCR_017376 | Primer Express Software v3.0.1, Primer Express™ Software v3.0.1 License, Primer Express™ Software v3.0.1 | 2026-09-19 12:56:07 | 6 | ||||||||||
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4D Nucleome Resource Report Resource Website 10+ mentions |
4D Nucleome (RRID:SCR_016925) | data or information resource, portal, project portal | Research project to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development and diseases. Portal provides free access to datasets, software packages, and protocols to advance biomedical research of nuclear architecture. Aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes. | nuclear, organization, gene, expression, cellular, function, normal, development, disease, map, structure, human, mouse, genome |
is listed by: NIDDK Information Network (dkNET) is related to: International Human Epigenome Consortium |
NIH Common Fund | PMID:28905911 | Public | SCR_016925 | 4D Nucleome Network; 4DN Web Portal, The 4D nucleome project, 4DN Portal | 2026-09-19 12:56:06 | 30 | |||||||
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Digital Expression Explorer 2 Docker Image Resource Report Resource Website 1+ mentions |
Digital Expression Explorer 2 Docker Image (RRID:SCR_016931) | data processing software, software application, software resource | Docker image that is used to process all of the data present in the Digital Expression Explorer 2 dataset. It can be freely used by anyone to process data on NCBI SRA or process their own RNA-seq fastq files. Used for bulk reprocessing of public RNA-seq data from SRA. The pipeline tallies the reads assigned to each gene or transcript. | transcriptome, pipeline, bulk, reprocess, public, RNAseq, data, SRA, gene, read |
is related to: Digital Expression Explorer 2 Project is related to: Digital Expression Explorer 2 Source Code |
DOI:10.5281/zenodo.1561840 | Free, Registration required | SCR_016931 | 2026-09-19 12:56:06 | 1 | |||||||||
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mirDIP Resource Report Resource Website 100+ mentions |
mirDIP (RRID:SCR_016770) | data or information resource, database, portal | microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies. | data, integral, portal, DIP, collect, predict, microRNA, gene, human | Canada Foundation for Innovation ; Canadian Cancer Society Research Institute ; Krembil Foundation ; Natural Sciences Research Council ; Ontario Research Fund |
PMID:29194489 | Free, Download available, Freely available, email address required to download, Acknowledgement requested | SCR_016770 | mirDIP 4.1, mirDIP, microRNA Data Integration Portal | 2026-09-19 12:56:06 | 229 |
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