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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software library, software toolkit, software resource | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-08-12 10:53:09 | 1 | ||||||
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MAXFLOW Resource Report Resource Website 1+ mentions |
MAXFLOW (RRID:SCR_024103) | software library, software toolkit, software resource | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-08-12 10:53:03 | 1 | |||||||
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arcasHLA Resource Report Resource Website 1+ mentions |
arcasHLA (RRID:SCR_022286) | data processing software, software resource, software application | Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq. | in silico inference of HLA genotypes, RNA-seq data, HLA typing | DARPA ; Phillip A. Sharp award ; NCI U54CA193313; NIGMS R01GM117591 |
PMID:31173059 | Free | SCR_022286 | 2026-08-12 10:52:52 | 8 | |||||||||
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Parsnp Resource Report Resource Website 50+ mentions |
Parsnp (RRID:SCR_024153) | software library, software toolkit, software resource | Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction. | align core genome, bacterial genomes, | is listed by: Debian | PMID:25410596 | Free, Available for download, Freely available, | OMICS_21461 | https://sources.debian.org/src/parsnp/, https://github.com/marbl/parsnp | SCR_024153 | parsnp | 2026-08-12 10:53:10 | 54 | ||||||
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PDB2PQR Resource Report Resource Website 1+ mentions |
PDB2PQR (RRID:SCR_024155) | software library, software toolkit, software resource | Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files. | interface for running PDB2PQR web service, prepare structures for further calculations, reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, generating PQR files, | is listed by: Debian | PMID:17488841 | Free, Available for download, Freely available, | OMICS_14370 | https://sources.debian.org/src/pdb2pqr/ | SCR_024155 | pdb2pqr | 2026-08-12 10:53:00 | 2 | ||||||
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PfTools Resource Report Resource Website 1+ mentions |
PfTools (RRID:SCR_024158) | software library, software toolkit, software resource | Software suite of tools to build and search generalized profiles. | build and search generalized profiles, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_29588 | https://sources.debian.org/src/pftools/ | SCR_024158 | pftools | 2026-08-12 10:53:00 | 3 | |||||||
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PhySamp Resource Report Resource Website 1+ mentions |
PhySamp (RRID:SCR_024159) | software library, software toolkit, software resource | Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree. | phylogenetic sampling, sample sequence alignment, corresponding phylogenetic tree, | is listed by: Debian | PMID:26055961 | Free, Available for download, Freely available, | OMICS_21686 | https://sources.debian.org/src/physamp/ | SCR_024159 | physamp | 2026-08-12 10:53:11 | 1 | ||||||
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BCALM 2 Resource Report Resource Website 1+ mentions |
BCALM 2 (RRID:SCR_023975) | source code, software resource, software application | Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution. | constructing compacted de Bruijn graph, sequencing data, | is listed by: Debian | PMID:27307618 | Free, Available for download, Freely available | OMICS_12164 | https://sources.debian.org/src/bcalm/ | SCR_023975 | bcalm | 2026-08-12 10:53:01 | 3 | ||||||
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Entrez Direct Resource Report Resource Website 10+ mentions |
Entrez Direct (RRID:SCR_024136) | software library, software toolkit, software resource | Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats. | access to NCBI's suite of interconnected databases, Unix terminal window, construct multi-step queries, retrive selected records, | is listed by: Debian | https://sources.debian.org/src/ncbi-entrez-direct/ | SCR_024136 | Entrez Direct: E-utilities on the Unix Command Line, EDirect, ncbi-entrez-direct | 2026-08-12 10:52:59 | 13 | |||||||||
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NJplot Resource Report Resource Website 1+ mentions |
NJplot (RRID:SCR_024137) | software library, software toolkit, software resource | Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. | tree drawing program, draw any phylogenetic tree, Newick phylogenetic tree format, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_04815 | https://sources.debian.org/src/njplot/ | SCR_024137 | njplot | 2026-08-12 10:53:10 | 2 | |||||||
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GeneTools Resource Report Resource Website 100+ mentions |
GeneTools (RRID:SCR_022505) | data processing software, image analysis software, software resource, software application | Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting. | Synoptics Ltd., Syngene, chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging, colony counting. | is listed by: SoftCite | Restricted | SCR_022505 | 2026-08-12 10:52:44 | 201 | ||||||||||
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Prepare_SplicingPredictors Resource Report Resource Website 1+ mentions |
Prepare_SplicingPredictors (RRID:SCR_023316) | data processing software, software resource, software application | Software tool as set of scripts to prepare the input for several sequence-based RNA splicing methods from VCF files. | RNA splicing, sequence based models, prepare input from VCF files, | Fundação para a Ciência e a Tecnologia (FCT) Portugal | DOI:10.1101/2023.02.17.528928 | Free, Available for download, Freely available | SCR_023316 | 2026-08-12 10:53:01 | 1 | |||||||||
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NanoPlot Resource Report Resource Website 100+ mentions |
NanoPlot (RRID:SCR_024128) | software library, software toolkit, software resource | Software package as plotting tool for long read sequencing data and alignments. | plotting tool, long read sequencing data and alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanoplot/, https://nanoplot.bioinf.be/ | SCR_024128 | nanoplot | 2026-08-12 10:53:10 | 397 | ||||||||
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OBITools Resource Report Resource Website 10+ mentions |
OBITools (RRID:SCR_024141) | software library, software toolkit, software resource | Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. | analysing NGS data, DNA metabarcoding, filter and edit sequences, taxonomic annotation, analysis pipelines for DNA metabarcoding applications, | is listed by: Debian | PMID:25959493 | Free, Available for download, Freely available, | OMICS_32696 | https://sources.debian.org/src/obitools/ | SCR_024141 | obitools | 2026-08-12 10:53:04 | 39 | ||||||
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FreeImage Resource Report Resource Website 1+ mentions |
FreeImage (RRID:SCR_024022) | software library, software toolkit, software resource | Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. | support graphics image formats, PNG, BMP, JPEG, TIFF | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/freeimage/ | SCR_024022 | freeimage | 2026-08-12 10:53:01 | 2 | ||||||||
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Orthanc Resource Report Resource Website 1+ mentions |
Orthanc (RRID:SCR_024145) | software library, software toolkit, software resource | Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases. | DICOM server, medical imaging, | is listed by: Debian | PMID:29725964 | Free, Available for download, Freely available, | https://sources.debian.org/src/orthanc/ | SCR_024145 | orthanc | 2026-08-12 10:53:04 | 4 | |||||||
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GDCM Resource Report Resource Website 1+ mentions |
GDCM (RRID:SCR_024027) | software library, software toolkit, software resource | GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly. | set of tools to interface with existing medical database, file format definition, network communications protocol, | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/gdcm/ | SCR_024027 | Grassroots DICOM library, gdcm | 2026-08-12 10:53:08 | 2 | ||||||||
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OpenIGTLink Resource Report Resource Website 1+ mentions |
OpenIGTLink (RRID:SCR_024148) | software library, software toolkit, software resource | Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback. | Open Network Interface for Image-Guided Therapy, communication interface, image guided interventions, unified real-time communications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/openigtlink/ | SCR_024148 | , openigtlink, Open Network Interface for Image-Guided Therapy Link | 2026-08-12 10:53:04 | 2 | ||||||||
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BrainGlobe Atlas API Resource Report Resource Website 1+ mentions |
BrainGlobe Atlas API (RRID:SCR_023848) | bg-atlasapi | data processing software, software resource, software application | Software lightweight python module to interact with atlases for systems neuroscience. Provides consistent way to process brain atlas data from various sources. | Allen Mouse Brain Atlas, Allen Human Brain Atlas, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023848 | BrainGlobe Atlas API (bg-atlasapi) | 2026-08-12 10:52:53 | 4 | ||||||||
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Cell Ranger ARC Resource Report Resource Website 10+ mentions |
Cell Ranger ARC (RRID:SCR_023897) | data processing software, software resource, software application | Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX. | Chromium Single Cell Multiome ATAC, Gene Expression, sequencing data, processing sequencing data, gene expression analysis, chromatin accessibility analysis, | Restricted | SCR_023897 | 10x Genomics Cell Ranger ARC | 2026-08-12 10:53:07 | 23 |
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