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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | 2026-07-25 12:07:05 | 32 | ||||||||
|
SBARS Resource Report Resource Website |
SBARS (RRID:SCR_002371) | software resource | Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes. | linux, windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24532721 | OMICS_03432, biotools:sbars | https://bio.tools/sbars | SCR_002371 | S.B.A.R.S, S.B.A.R.S., S.B.A.R.S - Spectral-Based Approach for Repeats Search, Spectral-Based Approach for Repeats Search | 2026-07-25 12:05:21 | 0 | |||||||
|
CAMERA - Collection of annotation related methods for mass spectrometry data Resource Report Resource Website 1+ mentions |
CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) | CAMERA | software resource | A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. | standalone software, mac os x, unix/linux, windows, r, spectra, extraction, annotation, liquid chromatography, mass spectrometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22111785 | Free, Available for download, Freely available | biotools:camera, OMICS_03366 | https://bio.tools/camera | SCR_002466 | CAMERA - Collection of annotation related methods for mass spectrometry data | 2026-07-25 12:05:27 | 4 | |||||
|
PolyPhred Resource Report Resource Website 100+ mentions |
PolyPhred (RRID:SCR_002337) | PolyPhred | software resource | Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool. | windows, sequence, nucleotide substitution, heterozygote, polymorphic, genotype, single nucleotide polymorphism, fluorescence, single nucleotide substitution, polymorphism, insertion, deletion, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17115056 PMID:16493422 PMID:9207020 |
Free for academic use, Commercial use requires a license | biotools:polyphred, OMICS_01815 | https://bio.tools/polyphred | SCR_002337 | 2026-07-25 12:05:21 | 123 | ||||||
|
Iterative Signature Algorithm Resource Report Resource Website |
Iterative Signature Algorithm (RRID:SCR_002327) | isa2, ISA | software resource | A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix. | standalone software, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:12689096 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | biotools:isa, OMICS_03487 | https://bio.tools/isa | SCR_002327 | isa2: The Iterative Signature Algorithm | 2026-07-25 12:05:24 | 0 | |||||
|
libmgf Resource Report Resource Website |
libmgf (RRID:SCR_002664) | software resource | A flex/bison-based C++ Mascot Generic Format (MGF) parser library. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20334363 | Free, Available for download, Freely available | OMICS_03343, biotools:libmgf, BioTools:libmgf | https://bio.tools/libmgf, https://bio.tools/libmgf, https://bio.tools/libmgf | SCR_002664 | MGFp, libmgf (formerly MGFp) | 2026-07-25 12:05:32 | 0 | ||||||
|
ExomeDepth Resource Report Resource Website 100+ mentions |
ExomeDepth (RRID:SCR_002663) | software resource | Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | software package, unix/linux, mac os x, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: CRAN |
PMID:22942019 | Free, Available for download, Freely available | OMICS_05443, biotools:exomedepth | https://bio.tools/exomedepth | SCR_002663 | 2026-07-25 12:05:27 | 262 | |||||||
|
MethylAid Resource Report Resource Website 50+ mentions |
MethylAid (RRID:SCR_002659) | software resource | Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. | software package, illumina, mac os x, unix/linux, windows, r, dna methylation, gui, methylation array, microarray, quality control, two channel, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25147358 | Free, Available for download, Freely available | biotools:methylaid, OMICS_05457 | http://www.bioconductor.org/packages/release/bioc/html/MethylAid.html, http://shiny.bioexp.nl/MethylAid/, https://bio.tools/methylaid | SCR_002659 | MethylAid - Visual and interactive quality control of large Illumina 450k data sets, MethylAid: Visual and interactive quality control of large Illumina 450k data sets | 2026-07-25 12:05:27 | 65 | ||||||
|
libCSAM Resource Report Resource Website 1+ mentions |
libCSAM (RRID:SCR_002766) | software resource | Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24728856 | Free, Freely available, Available for download | OMICS_03750, biotools:libcsam | https://bio.tools/libcsam | SCR_002766 | 2026-07-25 12:05:30 | 1 | |||||||
|
RopeBWT2 Resource Report Resource Website 10+ mentions |
RopeBWT2 (RRID:SCR_002673) | software resource | A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:25107872 | Free, Available for download, Freely available | biotools:ropebwt2, OMICS_05300 | https://bio.tools/ropebwt2 | SCR_002673 | 2026-07-25 12:05:27 | 11 | |||||||
|
NetPathMiner Resource Report Resource Website 1+ mentions |
NetPathMiner (RRID:SCR_002757) | software resource | Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths. | software package, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25075120 | Free, Freely available, Available for download | biotools:netpathminer, OMICS_05210 | https://bio.tools/netpathminer | SCR_002757 | NetPathMiner: R package for network path mining through gene expression | 2026-07-25 12:05:30 | 3 | ||||||
|
GATE Resource Report Resource Website 100+ mentions |
GATE (RRID:SCR_002756) | data analysis resource | Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points. | chromatin state prediction software, time course epigenetic data, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23033340 | Free, Freely available, Available for download | OMICS_03065, biotools:gate | https://github.com/yu68/GATE, https://bio.tools/gate | SCR_002756 | Genomic Annotation from Time-couse Epigenomic data, Genomic Annotation from Time-couse Epigenomic data (GATE) | 2026-07-25 12:05:30 | 317 | ||||||
|
pNovo+ Resource Report Resource Website 1+ mentions |
pNovo+ (RRID:SCR_002860) | software resource | A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra. | mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:23272783 | Free, Freely available | biotools.pNovo_3, OMICS_02470 | https://bio.tools/pNovo_3 | SCR_002860 | 2026-07-25 12:05:33 | 7 | |||||||
|
covtobed Resource Report Resource Website |
covtobed (RRID:SCR_023998) | softwre application | Software tool to generate BED coverage tracks from BAM files. | generate BED coverage tracks, BAM files, | is listed by: Debian | DOI:10.21105/joss.02119 | Free, Available for download, Freely available | https://sources.debian.org/src/covtobed/ | SCR_023998 | 2026-07-25 12:10:35 | 0 | ||||||||
|
GNUmed Resource Report Resource Website |
GNUmed (RRID:SCR_024029) | software resource | Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists. | build Electronic Medical Record, multiple languages | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/gnumed-client/ | SCR_024029 | gnumed-client, gnumed-server, gnumed | 2026-07-25 12:10:35 | 0 | ||||||||
|
Chemtool Resource Report Resource Website |
Chemtool (RRID:SCR_023992) | softwre application | Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11. | drawing organic molecules, drawing chemical structures, | is listed by: Debian | DOI:10.1002/nadc.20010491112 | Free, Available for download, Freely available | https://sources.debian.org/src/chemtool/ | SCR_023992 | chemtool | 2026-07-25 12:10:35 | 0 | |||||||
|
Entangle Resource Report Resource Website |
Entangle (RRID:SCR_024015) | softwre application | Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer. | tethered shooting, taking photographs with digital camera, computer controlled taking photographs, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/entangle/ | SCR_024015 | entangle | 2026-07-25 12:10:34 | 0 | ||||||||
|
FFP Resource Report Resource Website |
FFP (RRID:SCR_024018) | softwre application | Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison. | phylogenetic analysis, text comparison, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ffp/ | SCR_024018 | ffp, Feature Frequency Profile Phylogeny | 2026-07-25 12:10:33 | 0 | ||||||||
|
Dendroscope3 Resource Report Resource Website 10+ mentions |
Dendroscope3 (RRID:SCR_024003) | softwre application | Software Java program for analyzing and visualizing rooted phylogenetic trees and networks. | analyzing and visualizing rooted phylogenetic trees and networks, | is listed by: Debian | PMID:22780991 | Free, Available for download, Freely available | OMICS_04266 | https://sources.debian.org/src/dendroscope/ | SCR_024003 | dendroscope, dendroscope3 | 2026-07-25 12:10:35 | 22 | ||||||
|
yaha Resource Report Resource Website |
yaha (RRID:SCR_024365) | aligment software | Software tool as fast and flexible long read alignment with optimal breakpoint detection. | fast and flexible long-read alignment, optimal breakpoint detection, | is listed by: Debian | PMID:22829624 | Free, Available for download, Freely available, | OMICS_04675 | https://sources.debian.org/src/yaha/ | SCR_024365 | YAHA | 2026-07-25 12:10:37 | 0 |
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