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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Easyfig Resource Report Resource Website 1000+ mentions |
Easyfig (RRID:SCR_013169) | Easyfig | software resource | A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00907 | SCR_013169 | SciCrunch Registry | 2026-10-24 12:47:00 | 1209 | ||||||||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | SciCrunch Registry | 2026-10-24 12:47:03 | 320 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | SciCrunch Registry | Telescoper - De novo assembly algorithm | 2026-10-24 12:47:01 | 0 | ||||||
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | SciCrunch Registry | 2026-10-24 12:47:01 | 6 | |||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | SciCrunch Registry | 2026-10-24 12:47:01 | 0 | ||||||||
|
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 | SciCrunch Registry | heurAA - NGS multiplexed amplicon aligner | 2026-10-24 12:47:01 | 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 | SciCrunch Registry | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-10-24 12:47:00 | 0 | ||||||||
|
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 | SciCrunch Registry | SeqTRACS: LIMS for sequencing core facilities | 2026-10-24 12:47:03 | 0 | |||||||
|
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 | SciCrunch Registry | 2026-10-24 12:47:02 | 91 | ||||||||||
|
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 | SciCrunch Registry | denovo_solid_pipeline | 2026-10-24 12:47:01 | 0 | ||||||||
|
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 | SciCrunch Registry | Tuxedo: Automated RNA-sequencing Pipeline Script | 2026-10-24 12:47:02 | 103 | |||||||||
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | SciCrunch Registry | 2026-10-24 12:47:03 | 5 | ||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | analysis service resource, data analysis service, production service resource, service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | SciCrunch Registry | 2026-10-24 12:51:03 | 107 | |||||||||
|
OBO Tracker: Plant Ontology (PO) TERM requests Resource Report Resource Website 1+ mentions |
OBO Tracker: Plant Ontology (PO) TERM requests (RRID:SCR_006497) | OBO SF PO | data or information resource, database | Open Biomedical Ontologies Tracker that allows users to browse the Plant Ontology (PO) term requests and view their status. Details include a summary, ID, status, Date opened, assignee, submitter, resolution and assigned priority. New requests are accepted from logged in users. | plant, ontology, term |
is related to: OBO has parent organization: SourceForge |
The community can contribute to this resource, Account required | nlx_99576 | SCR_006497 | SciCrunch Registry | Tracker: PO TERM requests, Tracker: Plant Ontology TERM requests, SourceForge.net: Open Biomedical Ontologies: Plant Ontology (PO) TERM requests, Source Forge OBO Plant Ontology (PO) term request tracker, Tracker: Plant Ontology (PO) TERM requests | 2026-10-24 12:50:39 | 2 | |||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | SciCrunch Registry | 2026-10-24 12:52:05 | 35 | ||||||
|
MaryGold Resource Report Resource Website 1+ mentions |
MaryGold (RRID:SCR_000528) | MaryGold | software resource, software toolkit | Software package that enables detection of sequence variation between metagenomic samples. | sequence variation, metagenomic, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01495 | SCR_000528 | SciCrunch Registry | MaryGold - Variation analysis of metagenomic samples | 2026-10-24 12:49:46 | 1 | |||||||
|
Bioelectromagnetism Matlab Toolbox Resource Report Resource Website 1+ mentions |
Bioelectromagnetism Matlab Toolbox (RRID:SCR_006090) | data processing software, software application, software resource, software toolkit | Software toolbox to facilitate quick and easy import, visualization and measurement for Event Related Potential (ERP) data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive. | eeg, meg, mri, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ERPLAB has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
GNU General Public License | nif-0000-00268 | http://www.nitrc.org/projects/eeg | SCR_006090 | SciCrunch Registry | EEG Toolbox | 2026-10-24 12:49:52 | 1 | |||||||
|
MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | data processing software, software application, software resource, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | SciCrunch Registry | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-10-24 12:49:56 | 1320 | ||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software application, software resource | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | SciCrunch Registry | 2026-10-24 12:51:17 | 0 | ||||||
|
Magnolya Resource Report Resource Website 1+ mentions |
Magnolya (RRID:SCR_000164) | data analytics software, software application, software resource | A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets. | algorithm, copy number, next-generation, reference genome, dataset comparison |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23047563 | Free, Available for download, Freely available | OMICS_00347 | SCR_000164 | SciCrunch Registry | 2026-10-24 12:51:16 | 2 |
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