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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
pymzML Resource Report Resource Website 10+ mentions |
pymzML (RRID:SCR_002500) | software resource | Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: mzML has parent organization: University of Munster; North Rhine-Westphalia; Germany |
PMID:22302572 | Free, Available for download, Freely available | biotools:pymzml, OMICS_03355 | https://bio.tools/pymzml | SCR_002500 | 2026-02-14 02:00:17 | 18 | |||||||
|
sapFinder Resource Report Resource Website |
sapFinder (RRID:SCR_002685) | software resource | An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. | standalone software, r, mass spectrometry, proteomics, rna-seq, report writing, snp, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25053745 | Free, Available for download, Freely available | biotools:sapfinder, OMICS_05285 | https://bio.tools/sapfinder | SCR_002685 | sapFinder - A package for variant peptides detection and visualization in shotgun proteomics. | 2026-02-14 02:00:26 | 0 | ||||||
|
leeHom Resource Report Resource Website 50+ mentions |
leeHom (RRID:SCR_002710) | software resource | Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. | standalone software, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25100869 | Free, Available for download, Freely available | biotools:leehom, OMICS_05254 | https://bio.tools/leehom | SCR_002710 | 2026-02-14 02:00:26 | 53 | |||||||
|
Pathview Resource Report Resource Website 500+ mentions |
Pathview (RRID:SCR_002732) | software resource | A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23740750 | Free, Freely available, Available for download | biotools:pathview, OMICS_05212 | http://pathview.r-forge.r-project.org/ https://bio.tools/pathview |
SCR_002732 | path view | 2026-02-14 02:00:30 | 520 | ||||||
|
rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser https://bio.tools/rbiopaxparser |
SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-02-14 02:00:19 | 4 | ||||||
|
hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2026-02-14 02:00:33 | 6 | ||||||
|
tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-02-14 02:00:29 | 4 | ||||||
|
BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-02-14 02:00:21 | 44 | ||||||
|
PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm https://sources.debian.org/src/perm/ |
SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-02-14 02:00:38 | 60 | ||||||
|
SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-02-14 02:00:30 | 1294 | |||||
|
NovelSeq Resource Report Resource Website |
NovelSeq (RRID:SCR_003136) | NovelSeq | software resource | Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. | sequence, insertion, genome sequencing, genome, next-generation sequencing, illumina, unix, linux, c, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:20385726 | Free, Available for download, Freely available | biotools:novelseq, nlx_156791, OMICS_02164 | https://mybiosoftware.com/novelseq-1-0-2-sequence-insertions-detection.html#google_vignette | SCR_003136 | NovelSeq: Novel Sequence Insertion Detection | 2026-02-14 02:00:30 | 0 | |||||
|
mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-02-14 02:00:40 | 14 | ||||||
|
Pipeliner Resource Report Resource Website 1+ mentions |
Pipeliner (RRID:SCR_003171) | software resource | Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24890372 | Free, Available for download, Freely available | OMICS_04844, biotools:pipeliner | https://bio.tools/pipeliner | SCR_003171 | 2026-02-14 02:00:30 | 6 | |||||||
|
ALDEx2 Resource Report Resource Website 500+ mentions |
ALDEx2 (RRID:SCR_003364) | software resource | Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: aldex has parent organization: Western University; Ontario; Canada |
PMID:24910773 | Free, Available for download, Freely available | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2026-02-14 02:00:32 | 529 | |||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/ https://bio.tools/ggbio |
SCR_003313 | ggbio - Visualization tools for genomic data | 2026-02-14 02:00:45 | 14 | ||||||
|
PrimerSeq Resource Report Resource Website 1+ mentions |
PrimerSeq (RRID:SCR_003295) | PrimerSeq | software resource | Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species. | primer, rna-seq, rt-pcr, windows, mac os x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24747190 | Free, Available for download, Freely available | biotools:primerseq, OMICS_02328 | https://bio.tools/primerseq | SCR_003295 | Primer Seek in RNA-Seq | 2026-02-14 02:00:25 | 7 | |||||
|
MIPgen Resource Report Resource Website 10+ mentions |
MIPgen (RRID:SCR_003325) | software resource | Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline. | standalone software, c++, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:24867941 | Free, Available for download, Freely available | OMICS_04657, biotools:mipgen | https://github.com/shendurelab/MIPGEN https://bio.tools/mipgen |
SCR_003325 | MIPgen - One stop MIP design and analysis | 2026-02-14 02:00:46 | 48 | ||||||
|
Snakemake Resource Report Resource Website 100+ mentions |
Snakemake (RRID:SCR_003475) | Snakemake | software resource | A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. | python, workflow, bio.tools |
is used by: RiboSnake is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22908215 DOI:10.1093/bioinformatics/bts480 |
Free, Available for download, Freely available | OMICS_02299, biotools:snakemake | https://snakemake.github.io/ | SCR_003475 | snakemake - A Python based language and execution environment for make-like workflows | 2026-02-14 02:00:49 | 393 | |||||
|
PheWAS R Package Resource Report Resource Website 1+ mentions |
PheWAS R Package (RRID:SCR_003512) | software resource | Software package contains methods for performing Phenome-Wide Association Study. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:20335276 | Free | OMICS_00242, biotools:phewas | https://bio.tools/phewas | SCR_003512 | Phenome-Wide Association Study | 2026-02-14 02:00:28 | 6 | ||||||
|
Bpipe Resource Report Resource Website 10+ mentions |
Bpipe (RRID:SCR_003471) | Bpipe | software resource | Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. | genetics, dna, analysis, cluster, workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22500002 | Free, Available for download, Freely available | biotools:bpipe, OMICS_02301 | https://github.com/ssadedin/bpipe | SCR_003471 | bpipe - A tool for running and managing bioinformatics pipelines | 2026-02-14 02:00:49 | 13 |
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