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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ALBERT Resource Report Resource Website 10+ mentions |
ALBERT (RRID:SCR_009037) | ALBERT | software application, software resource | Software application that estimates genotype relative risks, genotyping error rates and population risk allele frequencies from marker genotype data in case-parent trios. ALBERT uses the distribution of trio marker genotypes to compute maximum likelihood estimates for the parameters. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:albert, nlx_154002 | https://bio.tools/albert | SCR_009037 | A Likelihood Based Estimation of Risk in Trios | 2026-07-26 09:04:42 | 47 | |||||||
|
FASTLINK Resource Report Resource Website 50+ mentions |
FASTLINK (RRID:SCR_009177) | FASTLINK | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, vms, ms-dos, .. and can also run in parallel on shared memory unix machines |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
PMID:8807326 | OMICS_28405, nlx_154309 | https://sources.debian.org/src/fastlink/ | SCR_009177 | faster version of LINKAGE LINKAGE | 2026-07-26 09:04:45 | 58 | ||||||
|
EXOMEPICKS Resource Report Resource Website 1+ mentions |
EXOMEPICKS (RRID:SCR_009174) | EXOMEPICKS | software application, software resource | Software application that suggests individuals to be sequenced in a large pedigree. ExomePicks assumes that a genotyping chip or another cost effective means will be used to determine IBD sharing in the pedigree and that, subsequently, one would like to sequence a minimal number of individuals and use their sequences together with IBD information to deduce the sequence of other individuals in the pedigree. We are currently using it in the context of whole exome and whole genome sequencing studies to pick individuals to be sequenced from large family collections. (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_154306, biotools:exomepicks | https://bio.tools/exomepicks | SCR_009174 | 2026-07-26 09:04:45 | 6 | ||||||||
|
DISENTANGLER Resource Report Resource Website 1+ mentions |
DISENTANGLER (RRID:SCR_009161) | DISENTANGLER | software application, software resource | Software application that is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, java/jre1.5, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154284, bIotools:disentangler | https://bio.tools/disentangler | SCR_009161 | 2026-07-26 09:04:45 | 4 | ||||||||
|
ALOHOMORA Resource Report Resource Website 1+ mentions |
ALOHOMORA (RRID:SCR_009117) | ALOHOMORA | software application, software resource | Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, ms-window, linux, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154219, biotools:alohomora | https://bio.tools/alohomora | SCR_009117 | 2026-07-26 09:04:51 | 8 | ||||||||
|
CASPAR Resource Report Resource Website 50+ mentions |
CASPAR (RRID:SCR_009074) | CASPAR | software application, software resource | Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:caspar, nlx_154071 | https://bio.tools/caspar | SCR_009074 | Computerized Affected Sibling Pair Analyzer and Reporter | 2026-07-26 09:04:43 | 52 | |||||||
|
genehunter-imprinting Resource Report Resource Website 1+ mentions |
genehunter-imprinting (RRID:SCR_009104) | GENEHUNTER-TWOLOCUS | software application, software resource | Resource no longer in service. Documented on February 23,2021.Software tool as modification of GENEHUNTER software package . Allows for parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. | gene, genetic, genomic, c, unix, sunos, solaris, osf, hpux, aix, ultrix, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
DOI:10.1086/302911 | Resource no longer in service. Documented on February 23,2021 | nlx_154199, biotools:genehunter-imprinting | https://bio.tools/genehunter-imprinting | http://www.staff.uni-marburg.de/~strauchk/software.html | SCR_009104 | GENEHUNTER-MODSCORE, GENEHUNTER-PLUS, GENEHUNTER, GENEHUNTER-IMPRINTING | 2026-07-26 09:04:44 | 1 | ||||
|
R/QTL Resource Report Resource Website 500+ mentions |
R/QTL (RRID:SCR_009085) | R/QTL | software application, software resource | Software program for mapping quantitative trait loci in experimental crosses. (entry from Genetic Analysis Software) | gene, genetic, genomic, c and r, unix, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btg112 | OMICS_07093, nlx_154097 | https://sources.debian.org/src/r-cran-qtl/ | SCR_009085 | 2026-07-26 09:04:50 | 987 | |||||||
|
CCREL Resource Report Resource Website |
CCREL (RRID:SCR_009142) | CCREL | software application, software resource | Software program for case-control genetic analysis that takes relatedness between individuals into account. It will perform single-marker and haplotypic tests, however it will only work with SNP or other biallelic markers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, perl, c, unix, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:ccrel, nlx_154261 | https://bio.tools/ccrel | SCR_009142 | Case-Control association analysis with RELlated individuals | 2026-07-26 09:04:52 | 0 | |||||||
|
LAMARC Resource Report Resource Website 10+ mentions |
LAMARC (RRID:SCR_009252) | LAMARC | software application, software resource | Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, ms-windows, macos |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: OMICtools |
DOI:10.1016/j.tree.2008.09.007 | OMICS_28408, nlx_154420 | https://sources.debian.org/src/lamarc/ | SCR_009252 | Likelihood Analysis with Metropolis Algorithm using Random Coalescence | 2026-07-26 09:04:56 | 46 | ||||||
|
HS-TDT Resource Report Resource Website 1+ mentions |
HS-TDT (RRID:SCR_009240) | HS-TDT | software application, software resource | Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154401, biotools:hs-tdt | https://bio.tools/hs-tdt | SCR_009240 | Haplotype Sharing Transmission Disequilibrium Test | 2026-07-26 09:04:55 | 4 | |||||||
|
SNPAAMapper Resource Report Resource Website |
SNPAAMapper (RRID:SCR_002012) | SNPAAMapper | software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take | single nucleotide polymorphism, amino acid, variant, annotation, exon, intron, mutation, next-generation sequencing, perl, downstream analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24250114 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01922, biotools:snpaamapper | https://bio.tools/snpaamapper | SCR_002012 | SNPAAMapper - A SNP Amino Acid Mapping tool | 2026-07-26 09:03:08 | 0 | |||||
|
HTqPCR Resource Report Resource Website 50+ mentions |
HTqPCR (RRID:SCR_003375) | HTqPCR | software application, software resource, data processing software | Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs). | data import, differential expression, gene expression, microtitre plate assay, multiple comparison, preprocessing, quality control, visualization, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19808880 | Free, Available for download, Freely available | biotools:htqpcr, OMICS_02314 | https://bio.tools/htqpcr | SCR_003375 | HTqPCR - Automated analysis of high-throughput qPCR data | 2026-07-26 09:03:25 | 74 | |||||
|
NanoStringNorm Resource Report Resource Website 100+ mentions |
NanoStringNorm (RRID:SCR_003382) | NanoStringNorm | software application, software resource, data processing software | Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis. | normalization, nanostring ncounter, mirna, mrna, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Ontario Institute for Cancer Research |
PMID:22513995 | Free, Available for download, Freely available | OMICS_02308, biotools:nanostringnorm | https://www.rdocumentation.org/packages/NanoStringNorm/versions/1.2.1.1/topics/NanoStringNorm | SCR_003382 | NanoStringNorm: Normalize NanoString miRNA and mRNA data | 2026-07-26 09:03:25 | 134 | |||||
|
skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | software application, software resource, data processing software | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer, https://sources.debian.org/src/skewer/, https://github.com/relipmoc/skewer | SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-07-26 09:03:01 | 11 | |||||
|
COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | software application, software resource, data processing software | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-07-26 09:04:39 | 164 | ||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software application, software resource, data processing software | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-07-26 09:04:28 | 0 | |||||||
|
epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | software application, software resource, data processing software | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-07-26 09:04:16 | 2 | |||||
|
SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-07-26 09:03:57 | 322 | ||||||
|
Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | software application, software resource, data processing software | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-07-26 09:05:12 | 1854 |
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