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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-08-01 12:01:20 | 14 | |||||
|
Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-08-01 12:01:20 | 22 | ||||||
|
SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-08-01 12:01:25 | 6 | ||||||
|
SNPiR Resource Report Resource Website 1+ mentions |
SNPiR (RRID:SCR_000557) | SNPiR | software resource | Software for reliable Identification of Genomic Variants Using RNA-seq Data. | genomic variant, rna-seq |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01362 | SCR_000557 | SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data | 2026-08-01 12:01:20 | 1 | |||||||
|
FPSAC Resource Report Resource Website 1+ mentions |
FPSAC (RRID:SCR_000555) | FPSAC | software resource | Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs. | genome, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:24068034 | biotools:fpsac, OMICS_00041 | https://bio.tools/fpsac | SCR_000555 | Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent, Fast Phylogenetic Scaffolding of Ancient Contigs, FPSAC: fast phylogenetic scaffolding of ancient contigs | 2026-08-01 12:01:15 | 1 | ||||||
|
RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/, https://posit.co/download/rstudio-desktop/ | http://www.rstudio.com/ | SCR_000432 | 2026-08-01 12:01:13 | 1034 | ||||||
|
drFAST Resource Report Resource Website 1+ mentions |
drFAST (RRID:SCR_000586) | drFAST | software resource | A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner. | di-base, solid color space, genome assemblies, memory-efficient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:21586516 | Free, Available for download, Freely available | biotools:drfast, OMICS_00661 | https://bio.tools/drfast | SCR_000586 | di-base read Fast Alignment Search Tool, drFAST: di-base read Fast Alignment Search Tool | 2026-08-01 12:01:21 | 1 | |||||
|
Genome BioInformatics Research Lab - gff2ps Resource Report Resource Website 1+ mentions |
Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format. | genome, sequence, visualization, parameters, bioinformatics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:11099262 DOI:10.1093/bioinformatics/16.8.743 |
Free, Available for download, Freely available | OMICS_17140, biotools:gff2ps, nif-0000-30611 | https://bio.tools/gff2ps, https://sources.debian.org/src/gff2ps/ | SCR_000462 | gff2ps | 2026-08-01 12:01:18 | 1 | ||||||
|
NGSmethPipe Resource Report Resource Website 1+ mentions |
NGSmethPipe (RRID:SCR_000583) | NGSmethPipe | software resource | A software tool which generates high-quality methylation maps. | computation, genomics, bioinformatics, methylation maps, visualization |
is listed by: OMICtools has parent organization: University of Granada; Granada; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00611 | SCR_000583 | NGSmethPipe - A tool to generate high-quality methylation maps | 2026-08-01 12:01:15 | 3 | |||||||
|
MAXCHELATOR Resource Report Resource Website 50+ mentions |
MAXCHELATOR (RRID:SCR_000459) | MAXC | software resource | A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration. | metal, concentration, chelator |
is related to: WEBMAXC STANDARD is related to: WEBMAXC EXTENDED has parent organization: Stanford University; Stanford; California |
PMID:8201981 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156862 | SCR_000459 | 2026-08-01 12:01:18 | 71 | |||||||
|
Neo Resource Report Resource Website 10+ mentions |
Neo (RRID:SCR_000634) | neo | software resource | A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion. | neurophysiology, electrophysiology, python, interoperability, intracellular, extracellular, eeg, electrode |
is used by: Elephant is used by: OpenElectrophy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:24600386 | Free, Available for download, Freely available | nlx_151874 | SCR_000634 | 2026-08-01 12:01:16 | 18 | |||||||
|
ContEst Resource Report Resource Website 1+ mentions |
ContEst (RRID:SCR_000595) | ContEst | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. | java, contamination, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:21803805 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01038, biotools:contest | https://bio.tools/contest | SCR_000595 | 2026-08-01 12:01:25 | 6 | ||||||
|
BLASR Resource Report Resource Website 10+ mentions Discontinued |
BLASR (RRID:SCR_000764) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Proovread |
PMID:22988817 DOI:10.1186/1471-2105-13-23 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:blasr, OMICS_05134 | https://bio.tools/blasr, https://sources.debian.org/src/blasr/ | SCR_000764 | Basic Local Alignment with Successive Refinement, BLASR: The PacBio long read aligner | 2026-08-01 12:01:18 | 15 | ||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-08-01 12:01:22 | 3 | |||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-08-01 12:01:23 | 3 | ||||||||
|
Sequencing Analysis Software Resource Report Resource Website 1+ mentions |
Sequencing Analysis Software (RRID:SCR_000718) | Sequencing Analysis Software | software resource | A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends. | basecall, capillary dna, quality control, low-quality sequence ends | is listed by: OMICtools | Restricted | OMICS_01814 | SCR_000718 | 2026-08-01 12:01:24 | 1 | ||||||||
|
NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-08-01 12:01:17 | 3 | |||||||
|
Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | OPERA-LG, Optimal Paired-End Read Assembler | 2026-08-01 12:01:27 | 3 | ||||||
|
RMAP Resource Report Resource Website 1+ mentions |
RMAP (RRID:SCR_000695) | RMAP | software resource | Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches. | next-generation sequencing, solexa |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:19736251 | OMICS_00681 | SCR_000695 | 2026-08-01 12:01:24 | 2 | ||||||||
|
TMAP Resource Report Resource Website 10+ mentions |
TMAP (RRID:SCR_000687) | TMAP | software resource | Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies. | next-generation sequencing | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00694 | SCR_000687 | TMAP - torrent mapping alignment program, Torrent Mapping Alignment Program | 2026-08-01 12:01:17 | 23 |
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