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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-08-08 12:00:20 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-08-08 12:00:20 | 0 | ||||||||
|
mGOASVM Resource Report Resource Website 1+ mentions |
mGOASVM (RRID:SCR_013098) | mGOASVM | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available. | subcellular localization, gram-negative protein, virus, protein |
is listed by: OMICtools has parent organization: Hong Kong Polytechnic University; Hong Kong; China |
PMID:23130999 | OMICS_01627 | SCR_013098 | 2026-08-08 11:59:52 | 4 | ||||||||
|
CEDER Resource Report Resource Website 10+ mentions |
CEDER (RRID:SCR_013255) | CEDER | software resource | R package intended to implement a program for detecting differentially expressed genes (DEG) using RNA-Seq by combining significance of exons within a gene. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
OMICS_01301 | SCR_013255 | 2026-08-08 12:00:20 | 11 | ||||||||||
|
QuantiSNP Resource Report Resource Website 50+ mentions |
QuantiSNP (RRID:SCR_013091) | QuantiSNP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Software to detect rare or de novo copy number alterations in normal DNA samples. Please note that QuantiSNP is no longer under active development. | matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17341461 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:quantisnp, OMICS_00730 | https://bio.tools/quantisnp | SCR_013091 | 2026-08-08 11:59:52 | 83 | ||||||
|
Celera Genome Browser Resource Report Resource Website |
Celera Genome Browser (RRID:SCR_013093) | Celera Genome Browser | software resource | Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00904 | SCR_013093 | 2026-08-08 12:00:07 | 0 | ||||||||
|
GPSeq Resource Report Resource Website 1+ mentions |
GPSeq (RRID:SCR_013250) | GPSeq | software resource | A software tool to analyze RNA-seq data to estimate gene and exon expression, identify differentially expressed genes, and differentially spliced exons., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01333 | SCR_013250 | 2026-08-08 11:59:54 | 6 | |||||||||
|
MAP Resource Report Resource Website 1+ mentions |
MAP (RRID:SCR_013216) | software resource | This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:22495746 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01424, biotools:MAP | https://bio.tools/MAP | SCR_013216 | Metagenomic Assembly Program | 2026-08-08 12:00:20 | 1 | ||||||
|
DiffSplice Resource Report Resource Website 10+ mentions |
DiffSplice (RRID:SCR_013215) | DiffSplice | software resource | The Genome-Wide Detection of Differential Splicing Events with RNA-seq. |
is listed by: OMICtools has parent organization: University of Kentucky; Kentucky; USA |
PMID:23155066 | OMICS_01330 | SCR_013215 | 2026-08-08 12:00:09 | 15 | |||||||||
|
genCAT Resource Report Resource Website 1+ mentions |
genCAT (RRID:SCR_013220) | genCAT | software resource | Software designed as an open platform that allows users to incorporate as many datasets (concepts) as possible to annotate the input gene list, as long as these datasets are prepared in bigwig, BED, BAM/SAM formats. |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v2 | OMICS_01416 | SCR_013220 | gencat - Gene''s Comprehensive Annotation Tool | 2026-08-08 12:00:20 | 6 | ||||||||
|
SOCS Resource Report Resource Website 50+ mentions |
SOCS (RRID:SCR_013223) | SOCS | software resource | Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00590 | SCR_013223 | 2026-08-08 11:59:53 | 91 | ||||||||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | software resource, software application, simulation software, data analysis software, data processing software | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-08-08 12:00:08 | 4723 | |||||
|
aCGH Resource Report Resource Website 100+ mentions |
aCGH (RRID:SCR_013232) | aCGH | software resource | Software functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00698 | SCR_013232 | 2026-08-08 11:59:53 | 136 | ||||||||||
|
DSP Resource Report Resource Website |
DSP (RRID:SCR_013114) | DSP | software resource | Pipeline for small genome assembly using SOLiD sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
Apache License, v2 | OMICS_00013 | SCR_013114 | denovo_solid_pipeline | 2026-08-08 12:00:07 | 0 | ||||||||
|
RepeatSeq Resource Report Resource Website 10+ mentions |
RepeatSeq (RRID:SCR_013235) | RepeatSeq | software resource | Software that determines genotypes for microsatellite repeats in high-throughput sequencing data. | is listed by: OMICtools | PMID:23090981 | OMICS_00112 | SCR_013235 | 2026-08-08 12:00:20 | 18 | |||||||||
|
Tuxedo Resource Report Resource Website 100+ mentions |
Tuxedo (RRID:SCR_013194) | Tuxedo | software resource | Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01415 | SCR_013194 | Tuxedo: Automated RNA-sequencing Pipeline Script | 2026-08-08 12:00:20 | 103 | |||||||||
|
MicroRazerS Resource Report Resource Website 1+ mentions |
MicroRazerS (RRID:SCR_013316) | MicroRazerS | software resource | A software tool optimized for mapping short RNAs onto a reference genome. |
is listed by: OMICtools has parent organization: Free University of Berlin; Berlin; Germany |
PMID:19880369 | OMICS_00371 | SCR_013316 | 2026-08-08 12:00:10 | 5 | |||||||||
|
FusionSeq Resource Report Resource Website 1+ mentions |
FusionSeq (RRID:SCR_013329) | FusionSeq | software resource | A modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data. | is listed by: OMICtools | OMICS_01351 | SCR_013329 | 2026-08-08 12:00:21 | 7 | ||||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | software resource, software application, data analysis software, data processing software | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-08-08 11:59:54 | 1418 | ||||
|
SeqTRACS Resource Report Resource Website |
SeqTRACS (RRID:SCR_013294) | SeqTRACS | software resource | Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01013 | SCR_013294 | SeqTRACS: LIMS for sequencing core facilities | 2026-08-08 11:59:54 | 0 |
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