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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ShrinkSeq Resource Report Resource Website 1+ mentions |
ShrinkSeq (RRID:SCR_012022) | ShrinkSeq | software resource | Software for detecting differential features across the entire spectrum, including the lower counts. | rna-seq, r |
is listed by: OMICtools has parent organization: VU University; Amsterdam; Netherlands |
PMID:22988280 | OMICS_01961 | SCR_012022 | 2026-08-29 11:24:14 | 2 | ||||||||
|
TSPM.R Resource Report Resource Website |
TSPM.R (RRID:SCR_012021) | TSPM.R | software resource | Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression. | r, rna-seq, gene expression | is listed by: OMICtools | OMICS_01960 | SCR_012021 | 2026-08-29 11:24:15 | 0 | |||||||||
|
GenomeJack Resource Report Resource Website 10+ mentions |
GenomeJack (RRID:SCR_012026) | GenomeJack | software resource | A genome browser specialized in next-generation sequencing data. | next-generation sequencing, genome, browser, analysis | is listed by: OMICtools | Free, Public | OMICS_02143 | SCR_012026 | 2026-08-29 11:24:14 | 35 | ||||||||
|
Standalone hamming Resource Report Resource Website |
Standalone hamming (RRID:SCR_012025) | Standalone hamming | software resource | Software for decoding error-correcting barcodes. | python, numpy, pyrosequencing, primer, ribosomal rna, dna barcoding, hamming code |
is listed by: OMICtools has parent organization: University of Colorado Boulder; Colorado; USA |
PMID:18264105 | OMICS_02117 | SCR_012025 | 2026-08-29 11:24:15 | 0 | ||||||||
|
FigTree Resource Report Resource Website 10000+ mentions |
FigTree (RRID:SCR_008515) | data processing software, data visualization software, software application, software resource | A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST. | data visualization software, graphical viewer, phylogenetic tree, annotate |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Edinburgh; Scotland; United Kingdom |
OMICS_04268, nif-0000-30567 | https://sources.debian.org/src/figtree/ | SCR_008515 | FigTree | 2026-08-29 11:23:31 | 12345 | ||||||||
|
SeqPig Resource Report Resource Website 1+ mentions |
SeqPig (RRID:SCR_008548) | SeqPig | software resource | A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24149054 | OMICS_01226 | SCR_008548 | 2026-08-29 11:23:07 | 2 | ||||||||
|
CAT Resource Report Resource Website 10+ mentions |
CAT (RRID:SCR_008421) | CAT | software resource | A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., 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 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01676, biotools:CAt | https://bio.tools/CAT | SCR_008421 | 2026-08-29 11:23:04 | 13 | |||||||
|
Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-08-29 11:23:30 | 3886 | |||||
|
Ultrasome Resource Report Resource Website |
Ultrasome (RRID:SCR_008465) | Ultrasome | software resource | An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:19228802 | Acknowledgement requested, Free for academic use | OMICS_00737 | SCR_008465 | 2026-08-29 11:23:05 | 0 | ||||||||
|
OligoPicker Resource Report Resource Website 1+ mentions |
OligoPicker (RRID:SCR_008720) | OligoPicker | software resource | Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting. | is listed by: OMICtools | PMID:12724288 | GNU General Public License, Acknowledgement requested | OMICS_00830 | SCR_008720 | 2026-08-29 11:23:11 | 3 | ||||||||
|
Biodoop Resource Report Resource Website |
Biodoop (RRID:SCR_008711) | Biodoop | software resource | A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop. | mapreduce/hadoop | is listed by: OMICtools | OMICS_01224 | SCR_008711 | 2026-08-29 11:23:23 | 0 | |||||||||
|
DrGaP Resource Report Resource Website 10+ mentions |
DrGaP (RRID:SCR_008670) | DrGaP | software resource | Designed to identify Driver Genes and Pathways in cancer genome sequencing studies. | is listed by: OMICtools | Cancer | OMICS_00149 | SCR_008670 | 2026-08-29 11:23:21 | 10 | |||||||||
|
InVEx Resource Report Resource Website 1+ mentions |
InVEx (RRID:SCR_008734) | InVEx | software resource | A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. |
is listed by: OMICtools has parent organization: Broad Institute |
OMICS_00151 | SCR_008734 | Introns Vs Exons | 2026-08-29 11:23:23 | 4 | |||||||||
|
PASTA Resource Report Resource Website 10+ mentions |
PASTA (RRID:SCR_008770) | PASTA | software resource | A complete pipeline for the analysis of alternative splicing using RNA-Sequencing data. |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
OMICS_01247 | SCR_008770 | Patterned Alignments for Splicing and Transcriptome Analysis | 2026-08-29 11:23:12 | 19 | |||||||||
|
QPALMA Resource Report Resource Website 1+ mentions |
QPALMA (RRID:SCR_008791) | QPALMA | software resource | An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454. | is listed by: OMICtools | OMICS_01248 | SCR_008791 | QPALMA: Optimal Spliced Alignments of Short Sequence Reads | 2026-08-29 11:23:25 | 1 | |||||||||
|
Sequgio Resource Report Resource Website |
Sequgio (RRID:SCR_008867) | Sequgio | software resource | An algorithm to estimate isoforms expression from RNA-seq data based on a model that doesn''t assume uniform distribution of count within transcripts. | is listed by: OMICtools | PMID:24307704 | OMICS_01290 | SCR_008867 | 2026-08-29 11:23:27 | 0 | |||||||||
|
YunBe Resource Report Resource Website |
YunBe (RRID:SCR_008740) | YunBe | software resource | A gene set analysis algorithm for biomarker identification in the cloud. | mapreduce/hadoop | is listed by: OMICtools | PMID:22084254 | OMICS_01227 | SCR_008740 | 2026-08-29 11:23:33 | 0 | ||||||||
|
Textpresso Resource Report Resource Website 10+ mentions |
Textpresso (RRID:SCR_008737) | Textpresso | data or information resource, database, software application, software resource, text-mining software | An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text. | literature, extract, process, bibliographic resource, database application, linux, macos, pdf, perl, posix/unix-like, sh, bash, unix shell, web service, search engine, curation tool, dicty, neuroscience, regulon db, ecoliwiki, ecocyc, curation, text-mining |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: WormBase is related to: Dictyostelium discoideum genome database |
NHGRI HG004090 | PMID:18949581 PMID:15383839 |
Textpresso License | nlx_143812, OMICS_01199 | http://www.nitrc.org/projects/textpresso-2-0/ | SCR_008737 | Text presso, Textpresso - literature search engine | 2026-08-29 11:23:23 | 10 | ||||
|
FGDP Resource Report Resource Website |
FGDP (RRID:SCR_008910) | FGDP | software resource | A Java-based, Microarray or Genechip data analysis system. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Fox Chase Cancer Center |
PMID:14734324 | GNU General Public License | OMICS_00756, biotools:fgdp | https://bio.tools/fgdp | SCR_008910 | Functional Genomics Data Pipeline (FGDP), Functional Genomics Data Pipeline | 2026-08-29 11:23:15 | 0 | |||||
|
A sample size calculation method Resource Report Resource Website |
A sample size calculation method (RRID:SCR_009469) | A sample size calculation method | software resource | Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. R code is available from the corresponding author. | is listed by: OMICtools | PMID:24314022 | OMICS_01228 | SCR_009469 | 2026-08-29 11:23:18 | 0 |
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