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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | data analysis software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 1553 | |||||||||
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TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | data analysis software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 4 | ||||||||||
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Ocular Resource Report Resource Website 1+ mentions |
Ocular (RRID:SCR_024490) | data acquisition software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 4 | |||||||||
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Umediation Resource Report Resource Website 1+ mentions |
Umediation (RRID:SCR_024492) | data analysis software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 1 | |||||||||
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IntFOLD Resource Report Resource Website 1+ mentions |
IntFOLD (RRID:SCR_024523) | data access protocol, software resource, web service | 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 | 2026-09-12 01:00:48 | 8 | |||||||||
|
OMNISEC Resource Report Resource Website 10+ mentions |
OMNISEC (RRID:SCR_024485) | data analysis software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 39 | ||||||||||
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PHYLDOG Resource Report Resource Website 1+ mentions |
PHYLDOG (RRID:SCR_024487) | data analysis software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 1 | |||||||||
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ASTRAL-Pro Resource Report Resource Website 1+ mentions |
ASTRAL-Pro (RRID:SCR_024520) | simulation software, software application, 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 | 2026-09-12 01:00:48 | 3 | ||||||||
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Kaplan Meier Plotter Resource Report Resource Website 1+ mentions |
Kaplan Meier Plotter (RRID:SCR_024521) | data access protocol, software resource, web service | 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 | 2026-09-12 01:00:48 | 6 | |||||||
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ProgRes Capture Pro Resource Report Resource Website 10+ mentions |
ProgRes Capture Pro (RRID:SCR_024489) | data acquisition software, data processing software, software application, 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 | 2026-09-12 01:00:48 | 12 | ||||||||
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MADOKA Resource Report Resource Website 1+ mentions |
MADOKA (RRID:SCR_024522) | data access protocol, software resource, web service | 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 | 2026-09-12 01:00:48 | 1 | |||||||||
|
SPAdes Resource Report Resource Website 100+ mentions |
SPAdes (RRID:SCR_000131) | SPAdes | software resource, software toolkit | 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 | 2026-09-12 01:00:51 | 108 | |||
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riskRegression Resource Report Resource Website 10+ mentions |
riskRegression (RRID:SCR_024424) | software resource, software toolkit | Software R package provides risk regression models and prediction scores for survival analysis with competing risks. | risk prediction, risk regression models, prediction scores, survival analysis, competing risks, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tagteam/riskRegression | SCR_024424 | 2026-09-12 01:01:17 | 15 | |||||||||
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RapGreen Resource Report Resource Website 1+ mentions |
RapGreen (RRID:SCR_024426) | PMID:34568824 | software resource, software toolkit | Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package. | Phylogenetic tree management, phylogenetic tree analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/SouthGreenPlatform/rap-green/wiki, http://southgreenplatform.github.io/rap-green/ | SCR_024426 | 2026-09-12 01:01:17 | 1 | ||||||||
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ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software resource, software toolkit | Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot. | assessing overall diagnostic ability of binary classifier, evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024420 | Receiver Operating Characteristic it | 2026-09-12 01:01:17 | 1 | |||||||||
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Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software resource, software toolkit | Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats. | Translator library, geospatial data formats, Geospatial Data Abstraction Library bindings, | is listed by: SoftCite | Free, Available for download, Freely available | https://r-forge.r-project.org/projects/rgdal/ | SCR_024422 | , R geospatial data abstraction library, rgdal | 2026-09-12 01:01:17 | 6 | ||||||||
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survivalROC Resource Report Resource Website 10+ mentions |
survivalROC (RRID:SCR_024415) | software resource, software toolkit | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | survival Receiver Operating Characteristic | 2026-09-12 01:01:17 | 23 | |||||||||
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ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software resource, software toolkit | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | 2026-09-12 01:01:18 | 8 | |||||||||
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gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software resource, software toolkit | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | 2026-09-12 01:01:18 | 4 | ||||||||||
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Inference of CRISPR Edits Resource Report Resource Website 100+ mentions |
Inference of CRISPR Edits (RRID:SCR_024508) | ICE | analysis service resource, production service resource, service resource, software resource | Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data. | analysis of CRISPR editing data, CRISPR editing analysis, | is listed by: SoftCite | PMID:35119294 | Free, Freely available | https://github.com/synthego-open/ice#ref2 | SCR_024508 | Synthego Inference of CRISPR Edits | 2026-09-12 01:01:18 | 103 |
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