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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Oases Resource Report Resource Website 100+ mentions |
Oases (RRID:SCR_011896) | Oases | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. | bio.tools, transcriptome assembler |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
DOI:10.1093/bioinformatics/bts094 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:oases, OMICS_01322 | https://bio.tools/oases | https://sources.debian.org/src/oases/ | SCR_011896 | 2026-02-07 02:08:18 | 289 | |||||
|
TopHat-Fusion Resource Report Resource Website 100+ mentions |
TopHat-Fusion (RRID:SCR_011899) | TopHat-Fusion | software resource | An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21835007 | OMICS_01359, biotools:tophat-fusion | https://bio.tools/tophat-fusion | SCR_011899 | TopHat-Fusion: An algorithm for Discovery of Novel Fusion Transcripts | 2026-02-07 02:08:18 | 156 | ||||||
|
BLAT Resource Report Resource Website 1000+ mentions |
BLAT (RRID:SCR_011919) | BLAT | software resource | Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. | bio.tools |
is used by: deFuse is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA is required by: RelocaTE |
biotools:blat, OMICS_01434 | https://bio.tools/blat | SCR_011919 | 2026-02-07 02:08:27 | 3674 | ||||||||
|
BBSeq Resource Report Resource Website 1+ mentions |
BBSeq (RRID:SCR_011877) | BBSeq | software resource | A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
biotools:bbseq, OMICS_01300 | https://bio.tools/bbseq | SCR_011877 | 2026-02-07 02:08:17 | 3 | ||||||||
|
IDBA-UD Resource Report Resource Website 100+ mentions |
IDBA-UD (RRID:SCR_011912) | IDBA-UD | software resource | Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. |
is listed by: OMICtools is listed by: Debian is related to: Meta-IDBA |
PMID:22495754 DOI:10.1093/bioinformatics/bts174 |
Acknowledgement requested | OMICS_01423 | https://sources.debian.org/src/idba/ | SCR_011912 | 2026-02-07 02:08:18 | 496 | |||||||
|
Oncofuse Resource Report Resource Website 10+ mentions |
Oncofuse (RRID:SCR_011904) | Oncofuse | software resource | Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1093/bioinformatics/btt445 | OMICS_01406 | https://sources.debian.org/src/oncofuse/ | SCR_011904 | 2026-02-07 02:08:24 | 13 | ||||||||
|
PRADA Resource Report Resource Website 10+ mentions |
PRADA (RRID:SCR_011906) | PRADA | software resource | A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01408, biotools:prada-rnaseq | https://bio.tools/prada-rnaseq | SCR_011906 | Pipeline for RNA-Sequencing Data Analysis | 2026-02-07 02:08:18 | 48 | |||||||
|
R-SAP Resource Report Resource Website 1+ mentions |
R-SAP (RRID:SCR_011907) | R-SAP | software resource | An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Georgia Institute of Technology; Georgia; USA |
OMICS_01409, biotools:r-sap | https://bio.tools/r-sap | http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm | SCR_011907 | 2026-02-07 02:08:26 | 3 | |||||||
|
RobiNA Resource Report Resource Website 10+ mentions |
RobiNA (RRID:SCR_011908) | RobiNA | software resource | Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure. | analyse Illumina/Solexa-based RNA-Seq data, data quality control, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22684630 | OMICS_01411 | SCR_011908 | 2026-02-07 02:08:24 | 19 | ||||||||
|
ArrayMiner Resource Report Resource Website 1+ mentions |
ArrayMiner (RRID:SCR_011955) | ArrayMiner | software resource | A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01570, biotools:arrayminer | https://bio.tools/arrayminer | SCR_011955 | 2026-02-07 02:08:20 | 2 | ||||||||
|
caftools Resource Report Resource Website |
caftools (RRID:SCR_023982) | software resource | Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site. | is listed by: Debian | Free, Available for download, Freely available | OMICS_24974 | https://sources.debian.org/src/caftools/ | SCR_023982 | 2026-02-07 02:11:48 | 0 | |||||||||
|
Conquest DICOM Resource Report Resource Website |
Conquest DICOM (RRID:SCR_023993) | softwre application | Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation. | DICOM training and testing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conquest/ | SCR_023993 | conquest-common, conquest-dbase, conquest-postgres, conquest-dicom-server, conquest-sqlite, conquest-mysql | 2026-02-07 02:12:17 | 0 | ||||||||
|
CHIME Resource Report Resource Website |
CHIME (RRID:SCR_023987) | softwre application | Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation. | providing estimates, capacity planning, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/chime/ | SCR_023987 | COVID-19 Hospital Impact Model for Epidemics, chime | 2026-02-07 02:12:06 | 0 | ||||||||
|
EMMAX Resource Report Resource Website 1+ mentions |
EMMAX (RRID:SCR_024012) | softwre application | Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model. | statistical test, human or model organism association mapping, sample structure, association mapping | is listed by: Debian | Free, Available for download, Freely available | OMICS_08871 | https://sources.debian.org/src/emmax/ | SCR_024012 | Efficient Mixed-Model Association eXpedited, emmax | 2026-02-07 02:12:06 | 2 | |||||||
|
dicompyler Resource Report Resource Website |
dicompyler (RRID:SCR_024006) | softwre application | Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer. | radiation therapy research platform, DICOM standard, cross platform DICOM RT viewer, | is listed by: Debian | DOI:10.1118/1.3468652 | Free, Available for download, Freely available | https://sources.debian.org/src/dicompyler/ https://github.com/bastula/dicompyler |
SCR_024006 | 2026-02-07 02:12:17 | 0 | ||||||||
|
foreign Resource Report Resource Website |
foreign (RRID:SCR_024025) | softwre application | Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files. | Reading and writing data, 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', reading and writing some 'dBase' files, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/foreign/ | SCR_024025 | r-cran-foreign | 2026-02-07 02:12:06 | 0 | ||||||||
|
Deepbinner Resource Report Resource Website |
Deepbinner (RRID:SCR_024001) | softwre application | Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads. | signal level demultiplexer, Oxford Nanopore reads, demultiplexing barcoded Oxford Nanopore sequencing reads, | is listed by: Debian | PMID:30458005 | Free, Available for download, Freely available | OMICS_30643 | https://sources.debian.org/src/deepbinner/ | SCR_024001 | deepbinner | 2026-02-07 02:12:17 | 0 | ||||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., 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: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-02-07 02:07:50 | 462 | |||||||
|
CRAC Resource Report Resource Website 10+ mentions |
CRAC (RRID:SCR_010652) | CRAC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1186/s12920-016-0178-5 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01240 | https://sources.debian.org/src/crac/ | SCR_010652 | 2026-02-07 02:07:49 | 16 | |||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-02-07 02:07:53 | 8 |
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