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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ANNOVAR Resource Report Resource Website 5000+ mentions |
ANNOVAR (RRID:SCR_012821) | ANNOVAR | software application, software resource | An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software) | genomic analysis, imaging genomics, next generation sequencing, snp, gene, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: wANNOVAR has parent organization: OpenBioinformatics.org |
PMID:20601685 | Free | nlx_154225, biotools:annovar, OMICS_00165 | https://bio.tools/annovar https://bio.tools/annovar |
SCR_012821 | functional ANNOtation of genetic VARiants, ANNOVAR: Functional annotation of genetic variants | 2026-02-15 09:20:40 | 5946 | |||||
|
ScanProsite Resource Report Resource Website 10+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | web service, data access protocol, software resource | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government ; |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | 2026-02-15 09:23:31 | 44 | |||||||
|
PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | software application, data processing software, data analysis software, software resource | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | 2026-02-15 09:23:31 | 13 | ||||||||||
|
ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | software application, data processing software, data analysis software, software resource | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-02-15 09:23:43 | 228 | |||||||||
|
pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | software application, simulation software, software resource | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-02-15 09:23:31 | 23 | ||||||||
|
VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | software application, data processing software, data analysis software, software resource | Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. | processing and preparing metagenomics, genomics and population genomics, nucleotide sequence data, | is listed by: SoftCite | PMID:27781170 | Free, Available for download, Freely available | SCR_024494 | 2026-02-15 09:22:43 | 1348 | |||||||||
|
TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | software application, data processing software, data analysis software, software resource | Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data. | Tomocube, Inc., Daejeon, . Republic of Korea, visualization and analysis of RI tomograms, color code the image, | is listed by: SoftCite | Restricted | SCR_024498 | 2026-02-15 09:22:43 | 3 | ||||||||||
|
Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | software application, data processing software, data acquisition software, software resource | Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system. | Teledyne Photometrics, image acquisition, capture high quality images and video, | is listed by: SoftCite | Restricted | SCR_024490 | Teledyne Photometrics Ocular | 2026-02-15 09:22:43 | 3 | |||||||||
|
Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | software application, data processing software, data analysis software, software resource | Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding. | simulate unmeasured confounding in mediation analysis, mediation analysis, unmeasured confounding, | is listed by: SoftCite | PMID:28724417 | Free, Available for download, Freely available | SCR_024492 | 2026-02-15 09:23:31 | 1 | |||||||||
|
IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | web service, data access protocol, software resource | Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences. | protein structure prediction, protein function prediction, modelling protein structures and functions from amino acid sequences, | is listed by: SoftCite | PMID:25820431 | Free, Freely available | SCR_024523 | 2026-02-15 09:23:34 | 3 | |||||||||
|
OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | software application, data processing software, data analysis software, software resource | Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL. | OMNISEC instrument control, data acquisition, analysis and reporting, proteins and polymers analysis, | is listed by: SoftCite | Restricted | SCR_024485 | 2026-02-15 09:23:44 | 38 | ||||||||||
|
PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | software application, data processing software, data analysis software, software resource | Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously. | probabilistic model, reconstruct species tree and all corresponding gene trees, build gene and species trees, gene families analysis, genomes analysis simultaneously, gene families duplications and losses, | is listed by: SoftCite | PMID:23132911 | Free, Freely available | SCR_024487 | 2026-02-15 09:23:33 | 1 | |||||||||
|
ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | software application, simulation software, software resource | Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy. | species tree reconstruction, reconstruction from multi-copy gene family trees | is listed by: SoftCite | PMID:32886770 | Free, Available for download, Freely available | SCR_024520 | ASTRAL for PaRalogs and Orthologs, ASTRAL-Pro 2 | 2026-02-15 09:23:31 | 3 | ||||||||
|
Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | web service, data access protocol, software resource | Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma. | survival analysis, assess correlation between expression of genes and survival, tumor samples, | is listed by: SoftCite | PMID:34309564 | Free, Freely available | http://kmplot.com/analysis/index.php?p=service&cancer=custom_plot | SCR_024521 | Kaplan-Meier Plotter, KM Plotter | 2026-02-15 09:23:45 | 4 | |||||||
|
ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | software application, data processing software, data acquisition software, software resource | Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras. | image acquisition, Jenoptik ProgRes microscope cameras, Jenoptik, | is listed by: SoftCite | PMID:34520656 | Free, Available for download, Freely available | SCR_024489 | Jenoptic ProgRes Capture Pro | 2026-02-15 09:23:44 | 12 | ||||||||
|
MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | web service, data access protocol, software resource | Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library. | large scale protein structure similarity searching, searching similar protein structures, aligning input structure with whole PDB library, | is listed by: SoftCite | PMID:31870277 | Free, Freely available | SCR_024522 | 2026-02-15 09:22:44 | 1 | |||||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software toolkit, software resource | Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | assembler, single, cell, small, genome, short, read, data |
is used by: shovill is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: rnaSPAdes is related to: rnaQUAST has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia works with: Illumina iSeq 100 Sequencing System |
Government of the Russian Federation ; NCRR P41 RR024851 |
PMID:24093227 PMID:22506599 DOI:10.1089/cmb.2012.0021 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01502 | https://sources.debian.org/src/spades/ | http://bioinf.spbau.ru/spades/ | SCR_000131 | SPAdes Genome Assembler | 2026-02-15 09:17:52 | 101 | |||
|
CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software toolkit, software resource | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-02-15 09:17:54 | 31 | ||||||||
|
BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-02-15 09:18:10 | 370 | ||||||
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Stereo Investigator Resource Report Resource Website 100+ mentions |
Stereo Investigator (RRID:SCR_002526) | instrument resource, software resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-02-15 09:18:19 | 145 |
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