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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Thermo Fisher: Nanodrop 1000 Spectrophotometer Resource Report Resource Website 50+ mentions |
Thermo Fisher: Nanodrop 1000 Spectrophotometer (RRID:SCR_016517) | instrument resource | Spectrophotometer for measurement and analysis of 1 ul samples with high accuracy and reproducibility. Full spectrum from 220nm to 750nm spectrophotometer utilizes patented sample retention technology that employs surface tension alone to hold sample in place. No need for cuvettes. Has capability to measure highly concentrated samples without dilution. | ABRF, spectrophotometer, nanodrop, concentration measurement, optical density, DNA, RNA, protein, nanodrop, instrument, equipment |
is listed by: USEDit works with: Thermo Scientific NanoDrop 1000 Software |
Commercially available | https://drive.google.com/file/d/1C1Dj_A1QxQibucCbFNues9EDZebDnx8K/view?usp=drivesdk | SCR_018035, Model_Number_Nanodrop_1000, SCR_020560 | https://www.marshallscientific.com/Nanodrop-ND-1000-Spectrophotometer-p/nd-1000.htm, https://www.selectscience.net/products/nanodrop-1000-spectrophotometer/?prodID=79482#tab-2, http://tools.thermofisher.com/content/sfs/manuals/nd-1000-v3.8-users-manual-8%205x11.pdf | SCR_016517 | NanoDrop 1000, Nanodrop ND-1000, Thermo Scientific NanoDrop 1000, NanoDrop 1000 Spectrophotometer | 2026-08-17 09:35:45 | 89 | ||||||
|
GCTF Resource Report Resource Website 100+ mentions |
GCTF (RRID:SCR_016500) | GCTF | data processing software, software resource, data analysis software, software application | Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | accurate, real, time, constrast, transfer, function, determination, correction, atomic, resolution, cryo, electron, microscopy, reconstruction, micrograph | is related to: University of Cambridge; Cambridge; United Kingdom | the Medical Research Council ; United Kingdom MC_UP_A025_1011; Wellcome Trust New Investigator Award |
PMID:26592709 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016500 | GContrast Transfer Function | 2026-08-17 09:35:47 | 101 | ||||||
|
Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, database, topical portal, portal, organism-related portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-08-17 09:35:36 | 5 | |||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data processing software, software resource, data analysis software, software application | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-08-17 09:35:41 | 39 | |||||||||
|
Praat Resource Report Resource Website 100+ mentions |
Praat (RRID:SCR_016564) | data processing software, software resource, data analysis software, software application | Software tool for phonetics research to analyse, synthesize, and manipulate speech. | phonetics, analyse, systhetize, speech | Free, Available for download, Freely available, Tutorial available | http://www.praat.org, https://github.com/praat/praat/blob/master/fon/manual_tutorials.cpp | SCR_016564 | 2026-08-17 09:35:38 | 123 | ||||||||||
|
circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data processing software, software resource, data analysis software, software application | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German National Academic Foundation ; German Ministry of Education ; Science ; Research and Technology |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-08-17 09:35:51 | 47 | |||||
|
nonparametricGGC_toolbox Resource Report Resource Website 1+ mentions |
nonparametricGGC_toolbox (RRID:SCR_016539) | nonparametricGGC | data processing software, software resource, data analysis software, software application | Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions. | nonparametric, Granger, causality, simulation, framework, code, estimate, brain, function | is related to: MATLAB | the Swiss National Science Foundation | Free, Available for download, Freely available | SCR_016539 | nonparametric Granger Geweke Causality | 2026-08-17 09:35:48 | 2 | |||||||
|
DCC Resource Report Resource Website 1+ mentions |
DCC (RRID:SCR_016544) | DCC | data processing software, software resource, data analysis software, software application | Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts. | databases, sequencing experiments, sequencing annotation, data annotation | Free, Available for download, Freely available | SCR_016544 | Data Coordination Center | 2026-08-17 09:35:45 | 1 | |||||||||
|
transfer_ learning_ ccnn Resource Report Resource Website 1+ mentions |
transfer_ learning_ ccnn (RRID:SCR_016590) | ccnn | data processing software, software resource, data analysis software, software application | Software program to implement transfer learning for a connectome convolutional neural network trained to classify functional connectomes using Tensorflow. | transfer, learning, connectome, convolutional, neural, network, functional, connectome, Tensorflow | uses: tensorflow | Free, Available for download, Freely available | SCR_016590 | connectome convolutional neural network, Connectome Convolutional Neural Network, CCNN | 2026-08-17 09:35:46 | 1 | ||||||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | data processing software, software resource, data visualization software, software application | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-08-17 09:35:39 | 29 | |||||
|
MutaGene Resource Report Resource Website 10+ mentions |
MutaGene (RRID:SCR_016574) | data processing software, software resource, data analysis software, software application | Software tool to explore and analyze mutagenic factors leading to tumors to decipher cancer genetic heterogeneity. | analyze, mutagenic, factor, turmor, decipher, cancer, genetic, heterogeneity | is listed by: OMICtools | National Library of Medicine ; NIH |
PMID:28472504 | Free, Available for download, Freely available | https://ncbiinsights.ncbi.nlm.nih.gov/tag/mutagene/ | SCR_016574 | 2026-08-17 09:35:38 | 10 | |||||||
|
kallisto Resource Report Resource Website 100+ mentions |
kallisto (RRID:SCR_016582) | data processing software, software resource, data analysis software, software application | Software tool for quantifying abundances of transcripts from RNA-Seq data or target sequences using high-throughput sequencing reads. | bio.tools |
is listed by: Debian is listed by: bio.tools works with: sleuth works with: kb_python |
PMID:27043002 | Free, Available for download, Freely available | biotools:kallisto | https://pachterlab.github.io/kallisto/download.html, https://bio.tools/kallisto, https://sources.debian.org/src/kallisto/ | SCR_016582 | kallisto v0.43.1 | 2026-08-17 09:35:38 | 148 | ||||||
|
smMIPfil Resource Report Resource Website 1+ mentions |
smMIPfil (RRID:SCR_016892) | data processing software, software resource, data analysis software, software application | Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required. | nucleotide, DNA, read, unique, molecular, identifier, single, inversion, probe, data, analysis, mutation, sequence | requires: SAMTOOLS | Free, Available for download, Freely available | SCR_016892 | single molecule Molecular Inversion Probesfil, smMIPfil | 2026-08-17 09:35:57 | 2 | |||||||||
|
ascat Resource Report Resource Website 10+ mentions |
ascat (RRID:SCR_016868) | ASCAT | data processing software, software resource, data analysis software, software application | Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data. | allele, specific, copy, number, analysis, tumor, purity, ploidy, sequencing, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:20837533 | Free, Available for download, Freely available | BioTools:ascat, biotools:ascat | https://github.com/VanLoo-lab/ascat, https://www.crick.ac.uk/research/labs/peter-van-loo/software, https://bio.tools/ascat, https://sources.debian.org/src/r-other-ascat/ | SCR_016868 | ASCAT 3.0, ASCAT 2.0, ASCAT 4.0, ASCAT 1.0, Allele-Specific Copy Number Analysis of Tumors, Allele Specific Copy Number Analysis of Tumors | 2026-08-17 09:35:48 | 42 | |||||
|
Pyclone Resource Report Resource Website 10+ mentions |
Pyclone (RRID:SCR_016873) | data processing software, software resource, data analysis software, software application | Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing. | infer, prevalence, point, mutation, heterogeneous, cancer, probabilistic, population, NGS, sequencing, data, analysis | PMID:24633410 | Available for download, Free for academic, nonprofit use | https://bitbucket.org/aroth85/pyclone/wiki/Home | SCR_016873 | PyClone | 2026-08-17 09:35:48 | 46 | ||||||||
|
Phenograph Resource Report Resource Website 100+ mentions |
Phenograph (RRID:SCR_016919) | PhenoGraph | data processing software, software resource, data analysis software, software application | Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. | high, dimention, single, cell, data, phenotype, analysis, heterogeneity |
uses: Python Programming Language is related to: Rphenograph |
NIGMS R00 GM104148; NICHD DP1 HD084071; NCI R01 CA164729; NCI U54 CA121852; NCI R01 CA130826; NCI U54 CA143907; US Department of Health and Human Services HHSN272200700038C; NIH N01 HV00242; NCI P01 CA034233; NIAID U19 AI057229; NCI U54 CA149145; US FDA HHSF223201210194C; US DOD W81XWH1210591; Entertainment Industry Foundation ; Rachford and Carlota Harris Endowed Professorship ; CIRM DR1 01477; CIRM RB201592; Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04; Packard Fellowship for Science and Engineering ; NIH Office of the Director DP2 OD002414 |
PMID:26095251 | Free, Available for download, Freely available | https://github.com/JinmiaoChenLab/Rphenograph | https://github.com/jacoblevine/PhenoGraph | SCR_016919 | 2026-08-17 09:35:48 | 235 | |||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data processing software, software resource, data analysis software, software application | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-08-17 09:35:41 | 114 | ||||||||
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rCASC Resource Report Resource Website 1+ mentions |
rCASC (RRID:SCR_017005) | data processing software, software resource, data analysis software, software application | Software package for reproducible classification analysis of single cell sequencing data. | reproducibility, classification, analysis, single, cell, sequencing, data, bio.tools |
is used by: Stardust is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
PMID:24204232 | Free, Available for download, Freely available | biotools:rCASC | https://kendomaniac.github.io/rCASC/, https://bio.tools/rCASC | SCR_017005 | rCASC, reproducible Cluster Analysis of Single Cells | 2026-08-17 09:36:00 | 1 | ||||||
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SwiftOrtho Resource Report Resource Website 1+ mentions |
SwiftOrtho (RRID:SCR_017122) | data processing software, software resource, data analysis software, software application | Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets. | orthology, analysis, identify, ortholog, paralog, co ortholog, genome, homology, different, species, large, dataset, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/543223 | Free, Available for download, Freely available | OMICS_30890, biotools:SwiftOrtho | https://bio.tools/SwiftOrtho | SCR_017122 | 2026-08-17 09:36:03 | 4 | |||||||
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cgpBattenberg Resource Report Resource Website 10+ mentions |
cgpBattenberg (RRID:SCR_017092) | data processing software, software resource, data analysis software, software application | Software tool as installation helper, perl wrapper and R program Battenberg which detects subclonality and copy number in matched NGS data. | installation, helper, perl, wrapper, detect, subclonality, copy, number, NGS, next, generation, sequencing, data | is related to: battenberg | Free, Available for download, Freely available | SCR_017092 | 2026-08-17 09:36:02 | 13 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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