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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MountainSort Resource Report Resource Website 10+ mentions |
MountainSort (RRID:SCR_017446) | data processing software, software resource, software application | Neurophysiological spike sorting software. | Neurophysiological, spike, sorting, BRAIN Initiative | is recommended by: BRAIN Initiative | NINDS NS090537 | Free, Available for download, Freely available | SCR_017446 | 2026-08-12 10:51:49 | 15 | |||||||||
|
hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | data processing software, software application, software toolkit, software resource | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-08-12 10:51:49 | 37 | |||||||
|
Scmap Resource Report Resource Website 10+ mentions |
Scmap (RRID:SCR_017338) | data processing software, software resource, software application | Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments. | Unsupervised, projection, single, cell, RNA-seq, data |
is listed by: Bioconductor has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:29608555 | Free, Available for download, Freely available | http://bioconductor.org/packages/scmap/, https://www.sanger.ac.uk/science/tools/scmap | SCR_017338 | 2026-08-12 10:51:45 | 17 | ||||||||
|
GeSeq Resource Report Resource Website 500+ mentions |
GeSeq (RRID:SCR_017336) | service resource, data processing software, software resource, software application | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-08-12 10:51:42 | 535 | ||||||
|
INCell Developer Toolbox Resource Report Resource Website 10+ mentions |
INCell Developer Toolbox (RRID:SCR_015790) | data processing software, image analysis software, software resource, software application | Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools. | INCell, HCA, cellular assay, advanced segmentation, image analysis, cellular imaging | Commercially available, Available for purchase | SCR_015790 | IN Cell Developer Toolbox v1.6, IN Cell Developer Toolbox | 2026-08-12 10:51:26 | 30 | ||||||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | data processing software, software resource, software application | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-08-12 10:51:24 | 1 | ||||
|
Neuron Tools Resource Report Resource Website 1+ mentions |
Neuron Tools (RRID:SCR_017450) | data processing software, software resource, software application | Software tools for converting data files into persistence diagrams and distance matrices. | Converting, data, file, diagram, distance, matice, BRAIN Initiative | is recommended by: BRAIN Initiative | NIBIB EB022899 | Free, Available for download, Freely available | SCR_017450 | 2026-08-12 10:51:47 | 3 | |||||||||
|
NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | data processing software, software resource, software application | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-08-12 10:51:38 | 331 | |||||||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software resource, software application | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-08-12 10:51:35 | 1 | ||||||
|
BrainVision Recorder Resource Report Resource Website 100+ mentions |
BrainVision Recorder (RRID:SCR_016331) | data processing software, software resource, software application | Software for multifunctional recording designed to provide Brain Products GmbH- Solutions for Neurophysiological Research amplifier with a platform for recording setup and execution. | multifunctional, recording, Brain Products GmbH Solutions for Neurophysiological Research, amplifier, platform, recording, execution, setup | Commercially available, Available for trial | SCR_016332 | http://pressrelease.brainproducts.com/recorder-tips/ | SCR_016331 | 2026-08-12 10:51:32 | 153 | |||||||||
|
DMT Normalization Resource Report Resource Website 1+ mentions |
DMT Normalization (RRID:SCR_017024) | data processing software, software resource, software application | Software tool for calculating optimal pretension conditions for microvascular or any small tubular tissue research. DMT Normalization Add-On, provided by ADInstruments, is included as part of LabChart Pro or can be purchased separately. | calculating, optimal, pretension, condition, microvascular, small, tubular, tissue | Commercially available | SCR_017024 | DMT Normalization Add-On | 2026-08-12 10:51:39 | 1 | ||||||||||
|
BASTA Resource Report Resource Website 1+ mentions |
BASTA (RRID:SCR_017303) | data processing software, software application, software toolkit, software resource | Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations. | Bayesian method, infer, migration, genetic, data, structured, coalescent, approximation, population | is related to: BEAST2 | DOI:10.1371/journal.pgen.1005421 | Free, Available for download, Freely available | SCR_017303 | BAyesian STructured coalescent Approximation, BASTA, BEAST2 | 2026-08-12 10:51:41 | 1 | ||||||||
|
GEOMAGIC Studio Resource Report Resource Website 1+ mentions |
GEOMAGIC Studio (RRID:SCR_016978) | GEOMAGIC Studio 12 | data processing software, software resource, software application | Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis. | 3D, scan, convert, data, surface, polygon, native, CAD, model | Free, Available for download, Freely available | https://de.3dsystems.com/press-releases/geomagic/studio-12-offers-fastest-way-to-convert-3d-scans-of-phy | SCR_016978 | 2026-08-12 10:51:41 | 1 | |||||||||
|
Albacore Resource Report Resource Website 100+ mentions |
Albacore (RRID:SCR_015897) | data processing software, software resource, software application | Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data. | sequence, dna, raw data, event detection, single-read, nanopore, basecaller, basecaller software, dockerfile | Free, Available for download | SCR_015897 | 2026-08-12 10:51:23 | 437 | |||||||||||
|
QDSpy Resource Report Resource Website 1+ mentions |
QDSpy (RRID:SCR_016985) | QDSpy | data processing software, software resource, software application | Software Python tool for scripting and presenting stimuli for visual neuroscience. | scripting, presenting, stimuli, visual, neuroscience | Free, Available for download, Freely available | http://qdspy.eulerlab.de/ | SCR_016985 | Quality Data System python software | 2026-08-12 10:51:38 | 7 | ||||||||
|
xHLA Resource Report Resource Website 1+ mentions |
xHLA (RRID:SCR_022277) | data processing software, software resource, software application | Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer. | HLA typing, short read sequence data, refines mapping results, amino acid level, four digit typing accuracy | NCI 5U24CA076518; NHLBI 5U10HL069294; Health Resources and Services Administration ; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | 2026-08-12 10:52:51 | 2 | |||||||||
|
GNU sed Resource Report Resource Website 1+ mentions |
GNU sed (RRID:SCR_018215) | data processing software, software resource, software application | Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file. | Text editor, filter text, modify text, pattern matching extraction, matching occurrences replaced, substitute occurrence, text processing | Free Software Foundation | Free, Available for download, Freely available | SCR_018215 | GNU stream editor | 2026-08-12 10:52:03 | 2 | |||||||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | standalone software, software application, software toolkit, software resource | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-08-12 10:52:09 | 1 | ||||||||
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GNU Grep Resource Report Resource Website 1+ mentions |
GNU Grep (RRID:SCR_018212) | data processing software, software resource, software application | Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options. | Print line, match pattern, input file, match search, pattern, plain text data, data set, match regular expression | Free, Freely available | SCR_018212 | GNU Grep 3.4, Grep | 2026-08-12 10:52:04 | 5 | ||||||||||
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DirectOverlay Resource Report Resource Website 1+ mentions |
DirectOverlay (RRID:SCR_018978) | data processing software, image analysis software, software resource, software application | Software package for display of light microscopy images together with atomic force microscopy images. | Light microscopy, light microscopy image, atomic force microscopy, image, atomic force, microscopy | Restricted | SCR_018978 | 2026-08-12 10:52:17 | 1 |
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