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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SP-Designer Resource Report Resource Website |
SP-Designer (RRID:SCR_000031) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. | standalone software, windows |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23634845 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03932 | SCR_000031 | SciCrunch Registry | 2026-11-07 11:53:50 | 0 | ||||||||
|
MysiRNA-designer Resource Report Resource Website |
MysiRNA-designer (RRID:SCR_000102) | software resource | Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22046244 | Free, Available for download, Freely available | OMICS_04748 | SCR_000102 | SciCrunch Registry | 2026-11-07 11:53:53 | 0 | ||||||||
|
dprimer Resource Report Resource Website |
dprimer (RRID:SCR_000050) | dprimer | software resource | A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample. | c++, command-line, pcr, primer, aligned sequence, degenerate primer | has parent organization: SourceForge | Free, Available for download, Freely available | OMICS_02342 | SCR_000050 | SciCrunch Registry | 2026-11-07 11:53:51 | 0 | ||||||||
|
iMethy Resource Report Resource Website |
iMethy (RRID:SCR_000049) | iMethy | software resource | Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing. | matlab | has parent organization: SourceForge | Free, Available for download, Freely available | OMICS_00628 | SCR_000049 | SciCrunch Registry | 2026-11-07 11:53:51 | 0 | ||||||||
|
Quant Resource Report Resource Website |
Quant (RRID:SCR_000267) | software resource | A software tool for the proteomics community that may help improving analysis of proteomic experimental data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17584939 | Free, Available for download, Freely available | OMICS_02504, biotools:quant | https://bio.tools/quant | SCR_000267 | SciCrunch Registry | 2026-11-07 11:53:56 | 0 | |||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | SciCrunch Registry | 2026-11-07 11:53:56 | 0 | |||||||
|
Grinder Resource Report Resource Website 1+ mentions |
Grinder (RRID:SCR_000168) | Grinder | software resource | An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities. | simulation, amplicon, shotgun, genomic sequencing, clinical, metagenomic, transcriptomic and metatranscriptomic |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22434876 DOI:10.1093/nar/gks251 |
Free, Available for download, Freely available | OMICS_01508 | https://sources.debian.org/src/grinder/ | SCR_000168 | SciCrunch Registry | 2026-11-07 11:53:53 | 3 | ||||||
|
OMSSAPercolator Resource Report Resource Website |
OMSSAPercolator (RRID:SCR_000287) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24504981 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02524 | SCR_000287 | SciCrunch Registry | 2026-11-07 11:53:57 | 0 | ||||||||
|
GProX Resource Report Resource Website 1+ mentions |
GProX (RRID:SCR_000273) | software resource | A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21602510 | Free, Available for download, Freely available | OMICS_02506 | SCR_000273 | SciCrunch Registry | Graphical Proteomics Data Explorer | 2026-11-07 11:53:55 | 1 | |||||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | SciCrunch Registry | 2026-11-07 11:53:58 | 4 | |||||||
|
COHCAP Resource Report Resource Website 10+ mentions |
COHCAP (RRID:SCR_006499) | COHCAP | software resource | An algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values. | java, perl, s/r, java swing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23598999 | Acknowledgement requested, Attribution Assurance License | biotools:cohcap, OMICS_00595 | https://bio.tools/cohcap | SCR_006499 | SciCrunch Registry | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-11-07 11:55:54 | 19 | |||||
|
GARM Resource Report Resource Website 10+ mentions |
GARM (RRID:SCR_006731) | GARM | software resource | A new software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01420 | SCR_006731 | SciCrunch Registry | Genome Assembler Reconcilation and Merging | 2026-11-07 11:56:00 | 12 | |||||||||
|
Blox Resource Report Resource Website 1+ mentions |
Blox (RRID:SCR_006667) | Blox | data processing software, data visualization software, image analysis software, software application, software resource | A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme | magnetic resonance imaging, diffusion tensor imaging, magnetic resonance spectroscopy, 3d visualization, brain, 3d rendering, neuroimaging, registration, segmentation, visualization, volume |
is listed by: Biositemaps has parent organization: SourceForge has parent organization: Kennedy Krieger Institute has parent organization: Johns Hopkins University; Maryland; USA |
GNU General Public License | nif-0000-00270 | http://pni.med.jhu.edu/blox/ | SCR_006667 | SciCrunch Registry | 2026-11-07 11:55:58 | 5 | |||||||
|
PowerMap Resource Report Resource Website 1+ mentions |
PowerMap (RRID:SCR_006721) | PowerMap | software resource | Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support. | neuroimaging, statistical analyses, false discovery rate, 3d spatial image, power calculation, sample size |
has parent organization: Wake Forest School of Medicine; North Carolina; USA has parent organization: SourceForge |
NINDS NS059793 | PMID:22644868 | Free, Public | nlx_152808 | SCR_006721 | SciCrunch Registry | 2026-11-07 11:56:00 | 3 | ||||||
|
Samscope Resource Report Resource Website |
Samscope (RRID:SCR_006715) | Samscope | software resource | A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. | c++, visualization, opengl, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00892 | SCR_006715 | SciCrunch Registry | samscope - A lightweight OpenGL SAM/BAM viewer | 2026-11-07 11:56:00 | 0 | |||||||
|
DMEAS Resource Report Resource Website 1+ mentions |
DMEAS (RRID:SCR_006679) | DMEAS | software resource | A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data. | c# |
is listed by: OMICtools has parent organization: SourceForge |
Creative Commons Attribution License | OMICS_00598 | SCR_006679 | SciCrunch Registry | DNA Methylation Entropy Analysis Software, DMEAS - DNA Methylation Entropy Analysis Software | 2026-11-07 11:56:00 | 2 | |||||||
|
HIA Resource Report Resource Website |
HIA (RRID:SCR_006865) | HIA | software resource | A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence. | matlab, java, command-line |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00666 | SCR_006865 | SciCrunch Registry | Hybrid Index based sequence Alignment, HIA - Hybrid Index based sequence Alignment | 2026-11-07 11:56:15 | 0 | ||||||||
|
fitGCP Resource Report Resource Website |
fitGCP (RRID:SCR_006741) | fitGCP | software resource | Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23589648 DOI:10.1093/bioinformatics/btt147 |
BSD License | OMICS_01046 | https://sources.debian.org/src/fitgcp/ | SCR_006741 | SciCrunch Registry | fitGCP - Fitting genome coverage distributions with mixture models | 2026-11-07 11:56:16 | 0 | ||||||
|
GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | SciCrunch Registry | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-11-07 11:56:01 | 3 | |||||
|
Next-gen Sequencing Scaffolding Tool Resource Report Resource Website |
Next-gen Sequencing Scaffolding Tool (RRID:SCR_006762) | Next-gen Sequencing Scaffolding Tool | software resource | Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00040 | SCR_006762 | SciCrunch Registry | 2026-11-07 11:56:01 | 0 |
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