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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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STAPLE Resource Report Resource Website 100+ mentions |
STAPLE (RRID:SCR_002590) | STAPLE | software application, software resource | An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | algorithm, analyze, c++, dicom, gifti, image display, linux, macos, microsoft, magnetic resonance, nifti, nrrd, posix/unix-like, quantification, rendering, segmentation, surface rendering, visualization, win32 (ms windows), windows, standard |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
PMID:15250643 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155994 | http://www.nitrc.org/projects/staple | SCR_002590 | Simultaneous Truth and Performance Level Estimation, STAPLE - Simultaneous Truth and Performance Level Estimation | 2026-08-09 09:03:36 | 142 | |||||
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CLUSTAG Resource Report Resource Website 1+ mentions |
CLUSTAG (RRID:SCR_001816) | CLUSTAG | software application, software resource | Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment. | gene, genetic, genomic, java, hierarchical clustering, single nucleotide polymorphism, windows, unix |
is listed by: Genetic Analysis Software has parent organization: Hong Kong Baptist University; Hong Kong; China |
PMID:15585525 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154273 | http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html | SCR_001816 | CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs | 2026-08-09 09:03:17 | 1 | |||||
|
Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software application, software resource | A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. | magnetic resonance, python, workflow, analysis, pipeline, interface, data processing, neuroimaging |
is used by: Forward: Accurate finite element electromagnetic head models is used by: fMRIPrep is used by: NHP BIDS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
PMID:21897815 | Free, Available for download, Freely available | nlx_155901 | http://www.nitrc.org/projects/nipype | SCR_002502 | Nipype: Neuroimaging in Python Pipeline and Interfaces, NIPY Pipeline and Interfaces | 2026-08-09 09:03:27 | 942 | |||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | data or information resource, atlas, reference atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-08-09 09:07:22 | 5 | |||||||||
|
Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System Resource Report Resource Website 10+ mentions |
Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) | instrument resource | Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C. | Matrix Assisted Laser Desorption Ionization Time of Flight Instrument, Instrument, Equipment, Applied Biosystems, USEDit, ABRF | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_018436.pdf | SCR_018448, SCR_019577, Model_Number_9700 | https://assets.thermofisher.com/TFS-Assets/LSG/manuals/cms_040970.pdf | SCR_018436 | 2026-08-09 09:07:14 | 13 | ||||||||
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DecodingDynamic Resource Report Resource Website 1+ mentions |
DecodingDynamic (RRID:SCR_021099) | data or information resource, source code, software resource | Data, code, and notebooks for replicating analyses reported in Rogers et al., Evidence for deep, distributed and dynamic semantic code in human ventral anterior temporal cortex. | ECoG, neural networks, semantics, replicating analyses, data, code, notebooks, human ventral anterior temporal cortex, semantic code | Medical Research Council Programme ; European Research Council |
DOI:10.1101/695049 | Free, Freely available | SCR_021099 | 2026-08-09 09:07:53 | 1 | |||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_022816) | data or information resource, atlas, reference atlas | Labels provide resource to isolate and identify mouse brain anatomical structures. Cell type specific transgenic mice and an MRI atlas were used to adjust and further segment the labels. Highly segmented anatomical labels in the adult mouse brain common coordinate framework. | isolate and identify mouse brain, brain anatomical structures, transgenic mice, MRI atlas, segment the labels | is used by: BICCN | Free, Freely available | SCR_022816 | Highly segmented anatomical labels in the adult mouse brain common coordinate framework. | 2026-08-09 09:08:05 | 5 | |||||||||
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fMOST Atlas Resource Report Resource Website |
fMOST Atlas (RRID:SCR_022868) | data or information resource, atlas, reference atlas | Reference atlas for mice. Contains both average and annotation templates. | reference atlas for mice, average and annotation templates | Free, Freely available | SCR_022868 | 2026-08-09 09:08:28 | 0 | |||||||||||
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Bio-EUtilities Resource Report Resource Website |
Bio-EUtilities (RRID:SCR_024064) | software toolkit, software resource | Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic. | interacting, storing information, NCBI's eUtils interface, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-eutilities-perl/ | SCR_024064 | Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils, libbio-eutilities-perl | 2026-08-09 09:08:54 | 0 | ||||||||
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Bio-Tools-Run-Alignment-Clustalw Resource Report Resource Website |
Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) | software toolkit, software resource | Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program. | performing multiple sequence alignment, set of unaligned sequences, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-run-alignment-clustalw-perl/ | SCR_024067 | libbio-tools-run-alignment-clustalw-perl, Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program | 2026-08-09 09:08:54 | 0 | ||||||||
|
Bio-Tools-Phylo-PAML Resource Report Resource Website |
Bio-Tools-Phylo-PAML (RRID:SCR_024069) | software toolkit, software resource | Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output. | parse output, PAML programs, codeml, baseml, basemlg, codemlsites, yn00. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-phylo-paml-perl/ | SCR_024069 | libbio-tools-phylo-paml-perl, Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml, baseml, codemlsites and yn00, basemlg | 2026-08-09 09:08:22 | 0 | ||||||||
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Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software toolkit, software resource | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-08-09 09:08:54 | 0 | ||||||||
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CLI for BioMAJ Resource Report Resource Website |
CLI for BioMAJ (RRID:SCR_023980) | software toolkit, software resource | Software package to use BioMAJ providing biomaj-cli. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biomaj3-cli/ | SCR_023980 | biomaj3-cli, biomaj-cli | 2026-08-09 09:08:51 | 0 | |||||||||
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CAT and BAT Resource Report Resource Website 1+ mentions |
CAT and BAT (RRID:SCR_023988) | software toolkit, software resource | Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies. | taxonomic classification, long DNA sequences, metagenome assembled genomes, known and unknown microorganisms, contemporary metagenomics studies, | is listed by: Debian | PMID:31640809 | Free, Available for download, Freely available | https://sources.debian.org/src/cat-bat/ | SCR_023988 | Bin Annotation Tool, Contig Annotation Tool, BAT, CAT, cat-bat, CAT/BAT | 2026-08-09 09:08:51 | 3 | |||||||
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NanoSV Resource Report Resource Website 1+ mentions |
NanoSV (RRID:SCR_024127) | software toolkit, software resource | Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers. | identify structural genomic variations, long-read sequencing data, Oxford Nanopore Technologies� MinION, GridION, PromethION, Pacific Biosciences RSII, Sequel sequencers. | is listed by: Debian | PMID:29109544 | Free, Available for download, Freely available, | OMICS_29732 | https://sources.debian.org/src/nanosv/ | SCR_024127 | nanosv | 2026-08-09 09:08:23 | 4 | ||||||
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GenomeTester4 Resource Report Resource Website 1+ mentions |
GenomeTester4 (RRID:SCR_024026) | software toolkit, software resource | Software toolkit for performing set operations - union, intersection and complement on k-mer lists. | performing set operations on k-mer lists, | is listed by: Debian | PMID:26640690 | Free, Available for download, Freely available, | OMICS_02363w | https://sources.debian.org/src/genometester/ | SCR_024026 | genometester | 2026-08-09 09:08:21 | 4 | ||||||
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Augur Resource Report Resource Website 50+ mentions |
Augur (RRID:SCR_023964) | software toolkit, software resource | Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines. | track evolution, sequence, serological data. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/augur/, https://docs.nextstrain.org/projects/augur/en/stable/ | SCR_023964 | augur | 2026-08-09 09:08:20 | 88 | ||||||||
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ExaBayes Resource Report Resource Website 1+ mentions |
ExaBayes (RRID:SCR_024019) | software toolkit, software resource | Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters. | Bayesian tree inference, large-scale analyses, computer clusters, | is listed by: Debian | PMID:25135941 | Free, Available for download, Freely available | OMICS_10303 | https://sources.debian.org/src/exabayes/ | SCR_024019 | exabayes | 2026-08-09 09:08:44 | 7 | ||||||
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CTK Resource Report Resource Website 1+ mentions |
CTK (RRID:SCR_024002) | software toolkit, software resource | Software to support biomedical image computing. | support biomedical image computing, biomedical image computing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/libctk-dev/ | SCR_024002 | CTK - The Common Tool Kit, ctk | 2026-08-09 09:08:52 | 2 | ||||||||
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pycoqc Resource Report Resource Website 10+ mentions |
pycoqc (RRID:SCR_024185) | software toolkit, software resource | Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data. | compute metrics, generate interactive QC plots, Oxford Nanopore technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pycoqc/ | SCR_024185 | 2026-08-09 09:08:48 | 24 |
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