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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks, https://bio.tools/cufflinks, https://sources.debian.org/src/cufflinks/ | SCR_014597 | 2026-08-05 10:46:11 | 8838 | |||||||
|
libRoadRunner Resource Report Resource Website 10+ mentions |
libRoadRunner (RRID:SCR_014763) | software application, simulation software, software resource | Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support. | simulation engine, simulation software, road runner, roadrunner, systems biology, synthetic biology |
is listed by: Debian is listed by: OMICtools |
NIGMS GM081070 | DOI:10.1093/bioinformatics/btv363 | Open source, Available for download | OMICS_09368 | https://sources.debian.org/src/libroadrunner-dev/ | SCR_014763 | 2026-08-05 10:46:12 | 11 | ||||||
|
Prokka Resource Report Resource Website 1000+ mentions |
Prokka (RRID:SCR_014732) | data processing software, software application, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotation, prokaryote, genome, prokaryotic genome, sequence analysis software, annotation software, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btu153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04220, biotools:prokka | https://bio.tools/prokka, https://sources.debian.org/src/prokka/, https://sources.debian.org/src/prokka/ | SCR_014732 | 2026-08-05 10:46:11 | 4876 | |||||||
|
SeaView Resource Report Resource Website 1000+ mentions |
SeaView (RRID:SCR_015059) | data processing software, software application, data visualization software, data analysis software, sequence analysis software, software resource | Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees. | sequence alignment, molecular phylogeny, phylogenetic tree, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:19854763 DOI:10.1093/molbev/msp259 |
Free, Available for download | OMICS_08908, biotools:seaview | https://bio.tools/seaview, https://sources.debian.org/src/seaview/ | SCR_015059 | 2026-08-05 10:46:15 | 1777 | |||||||
|
GIIRA Resource Report Resource Website 1+ mentions |
GIIRA (RRID:SCR_015507) | data processing software, software application, sequence analysis software, data analysis software, software resource | Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment. | gene prediction, rna seq, coding region, potential coding region |
is listed by: Debian is listed by: OMICtools |
DOI:10.1093/bioinformatics/btt577 | Available for download | OMICS_07360 | http://www.rki.de/EN/Content/Institute/DepartmentsUnits/JuniorGroups/JRG4.html, https://sources.debian.org/src/giira/ | SCR_015507 | 2026-08-05 10:46:25 | 3 | |||||||
|
SEER Resource Report Resource Website 100+ mentions |
SEER (RRID:SCR_015499) | data processing software, source code, software application, data analysis software, sequence analysis software, software resource | Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria. | bacterial genome association, sequence element enrichment analysis, kmer enrichment analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/ncomms12797 DOI:10.1101/038463 |
Available for download | OMICS_21699 | https://sources.debian.org/src/seer/ | SCR_015499 | 2026-08-05 10:46:25 | 463 | |||||||
|
Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | Parallel META, Parallel Meta | 2026-08-05 10:43:06 | 4 | |||||||
|
Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | software application, simulation software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | 2026-08-05 10:43:06 | 2 | ||||||||
|
RefFinder Resource Report Resource Website 10+ mentions |
RefFinder (RRID:SCR_000472) | RefFinder | analysis service resource, data access protocol, software resource, production service resource, service resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene expression, reference gene, web based tool |
uses: BestKeeper uses: NormFinder uses: geNORM is listed by: OMICtools has parent organization: East Carolina University; Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02321 | http://www.leonxie.com/referencegene.php | SCR_000472 | 2026-08-05 10:43:10 | 45 | |||||||
|
RSEM Resource Report Resource Website 50+ mentions |
RSEM (RRID:SCR_000262) | software resource, data processing software, software application, data analysis software | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-05 10:43:08 | 94 | ||||||
|
PSCBS Resource Report Resource Website |
PSCBS (RRID:SCR_000417) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. | abnormal copy number regions detection, allele specific DNA copy number data segmentation, |
is listed by: OMICtools is listed by: Debian is related to: CRAN has parent organization: University of California at San Francisco; California; USA |
PMID:21666266 DOI:10.1093/bioinformatics/btr329 |
Free, Available for download, Freely available | OMICS_05545 | https://sources.debian.org/src/r-cran-pscbs/ | SCR_000417 | PSCBS: Analysis of Parent-Specific DNA Copy Numbers | 2026-08-05 10:43:09 | 0 | ||||||
|
BSmooth-align Resource Report Resource Website 1+ mentions |
BSmooth-align (RRID:SCR_000013) | data processing software, image analysis software, software application, alignment software, data analysis software, software resource | Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements. | bisulfite sequence, read-level methylation, bisulfite sequence reads alignment, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01846 | SCR_000013 | 2026-08-05 10:43:05 | 1 | |||||||||
|
Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, standard specification, narrative resource, interchange format | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | Sequence Read Format (SRF) | 2026-08-05 10:43:06 | 1 | |||||||
|
GMATo Resource Report Resource Website 1+ mentions |
GMATo (RRID:SCR_000165) | data processing software, software application, sequence analysis software, data analysis software, software resource | A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable. | simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23861572 | Free, Available for download, Freely available | OMICS_00106 | SCR_000165 | Genome-wide Microsatellite Analyzing Tool, Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo) | 2026-08-05 10:43:07 | 1 | |||||||
|
DESeq Resource Report Resource Website 100+ mentions |
DESeq (RRID:SCR_000154) | DESeq | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression. | gene expression, binomial, differential, negative binomial distribution, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
PMID:20979621 DOI:10.1186/s13059-014-0550-8 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01306, biotools:deseq | https://bio.tools/deseq, https://sources.debian.org/src/r-bioc-deseq2/ | SCR_000154 | 2026-08-05 10:43:07 | 473 | ||||||
|
POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | software resource, data processing software, software application, data analysis software | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-08-05 10:43:10 | 0 | |||||
|
Glide Resource Report Resource Website 10+ mentions |
Glide (RRID:SCR_000187) | Glide | software application, simulation software, software resource | Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening. | ligand, receptor, docking, computation, virtual, screening, drug, discovery |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Ligprep |
PMID:18428795 | Restricted | OMICS_01601 | SCR_000187 | 2026-08-05 10:43:07 | 15 | |||||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | software resource, data processing software, software application, data analysis software | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | Geometric Analysis of Structural Variants | 2026-08-05 10:43:06 | 4 | ||||
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rtd Resource Report Resource Website |
rtd (RRID:SCR_000337) | software resource, data processing software, software application, data analysis software | Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes. | standalone software | is listed by: OMICtools | PMID:22675423 | Free, Available for download, Freely available | OMICS_03723 | SCR_000337 | 2026-08-05 10:43:09 | 0 | ||||||||
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ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | software resource, data processing software, software application, data analysis software | Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets. | chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02172 | SCR_000054 | ChIPmeta with HHM | 2026-08-05 10:43:05 | 0 |
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