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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReviSTER Resource Report Resource Website |
ReviSTER (RRID:SCR_012113) | software resource | Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23677944 | GNU General Public License | OMICS_05468 | SCR_012113 | Revise Simple Tandem repeat Error Reads | 2026-02-14 02:02:36 | 0 | |||||||
|
VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | 2026-02-14 02:02:18 | 11 | |||||||||
|
Pegasus-fus Resource Report Resource Website 10+ mentions |
Pegasus-fus (RRID:SCR_012118) | software resource | Software that annotates biologically functional gene fusion candidates. | standalone software, unix/linux, java, perl, python |
is used by: Cumulus is listed by: OMICtools has parent organization: SourceForge |
PMID:25183062 | OMICS_05584 | SCR_012118 | 2026-02-14 02:02:36 | 14 | |||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-02-14 02:02:18 | 8 | ||||||
|
iMSAT Resource Report Resource Website 1+ mentions |
iMSAT (RRID:SCR_012135) | software resource | A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs. | standalone software, illumina, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25281214 | OMICS_05873 | SCR_012135 | 2026-02-14 02:02:37 | 2 | |||||||||
|
NESmapper Resource Report Resource Website 1+ mentions |
NESmapper (RRID:SCR_012138) | software resource | A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25233087 | GNU General Public License | OMICS_05911 | SCR_012138 | 2026-02-14 02:02:18 | 6 | ||||||||
|
DHAC Resource Report Resource Website 1+ mentions |
DHAC (RRID:SCR_012139) | software resource | Software for clustering time-evolving networks. | standalone software, c++, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22689777 | GNU General Public License | OMICS_05923 | SCR_012139 | Dynamical Hierarchical Agglomerative Clustering | 2026-02-14 02:02:37 | 2 | |||||||
|
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 | City of Hope CpG Island Analysis Pipeline, COHCAP - City of Hope CpG Island Analysis Pipeline | 2026-02-14 02:01:19 | 18 | |||||
|
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 | Genome Assembler Reconcilation and Merging | 2026-02-14 02:01:22 | 11 | |||||||||
|
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 | 2026-02-14 02:01:14 | 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 | samscope - A lightweight OpenGL SAM/BAM viewer | 2026-02-14 02:01:22 | 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 | DNA Methylation Entropy Analysis Software, DMEAS - DNA Methylation Entropy Analysis Software | 2026-02-14 02:01:13 | 1 | |||||||
|
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 | Hybrid Index based sequence Alignment, HIA - Hybrid Index based sequence Alignment | 2026-02-14 02:01:14 | 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 | fitGCP - Fitting genome coverage distributions with mixture models | 2026-02-14 02:01:21 | 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 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-02-14 02:01:15 | 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 | 2026-02-14 02:01:23 | 0 | ||||||||||
|
QUASR Resource Report Resource Website 100+ mentions |
QUASR (RRID:SCR_006820) | QUASR | software resource | A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing. | next generation sequencing, python3, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01072 | SCR_006820 | QUASR - Cross-platform NGS processing and analysis pipeline in Python | 2026-02-14 02:01:14 | 213 | |||||||
|
simhtsd Resource Report Resource Website |
simhtsd (RRID:SCR_006822) | simhtsd | software resource | Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II. | command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2, v3 | OMICS_00256 | SCR_006822 | Simulate High-Throughput Sequencing Data | 2026-02-14 02:01:16 | 0 | |||||||
|
Virmid Resource Report Resource Website 1+ mentions |
Virmid (RRID:SCR_006780) | Virmid | software resource | A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion | somatic mutation, sample impurity, java, snp, variant, disease, control |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23987214 | OMICS_00095 | SCR_006780 | Virtual Microdissection for SNP calling | 2026-02-14 02:01:15 | 6 | |||||||
|
BIGpre Resource Report Resource Website |
BIGpre (RRID:SCR_006781) | BIGpre | software resource | A quality assessment software package for next-genomics sequencing data. | next generation sequencing, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22289480 | GNU General Public License, v3 | biotools:bigpre, OMICS_01035 | https://bio.tools/bigpre | SCR_006781 | 2026-02-14 02:01:23 | 0 |
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