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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ISMRMRD Resource Report Resource Website |
ISMRMRD (RRID:SCR_024043) | software library, software resource, software toolkit | Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format. | ISMRM Raw data format, C/C++ library for working with the format, | is listed by: Debian | PMID:26822475 | Free, Available for download, Freely available, | https://sources.debian.org/src/ismrmrd/ | SCR_024043 | ismrmrd, ISMRM Raw Data Format | 2026-08-07 09:30:09 | 0 | |||||||
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Phyx Resource Report Resource Website 1+ mentions |
Phyx (RRID:SCR_024164) | software library, software resource, software toolkit | Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects. | phylogenetic tools for unix, perform phylogenetics analyses on trees and sequences, C ++, explore phylogenetic objects, manipulate phylogenetic objects, analyze and simulate phylogenetic objects, | is listed by: Debian | PMID:28174903 | Free, Available for download, Freely available, | https://sources.debian.org/src/phyx/ | SCR_024164 | 2026-08-07 09:30:06 | 3 | ||||||||
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iVar Resource Report Resource Website 50+ mentions |
iVar (RRID:SCR_024045) | software resource, software toolkit | Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files. | call iSNVs from viral sequencing data, viral amplicon based sequencing, call iSNVs and consensus sequences from viral sequencing data, call iSNVs | is listed by: Debian | PMID:30621750 | Free, Available for download, Freely available, | https://sources.debian.org/src/ivar/, https://andersen-lab.github.io/ivar/html/ | SCR_024045 | ivar | 2026-08-07 09:30:09 | 77 | |||||||
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Plastimatch Resource Report Resource Website 10+ mentions |
Plastimatch (RRID:SCR_024168) | software library, software resource, software toolkit | Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images. | image computation, volumetric registration, segmentation, image processing, volumetric medical images, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/plastimatch/, https://gitlab.com/plastimatch/plastimatch | SCR_024168 | 2026-08-07 09:30:12 | 10 | |||||||||
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pngquant Resource Report Resource Website |
pngquant (RRID:SCR_024169) | software library, software resource, software toolkit | Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems. | lossy compression of PNG images, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pngquant/, https://github.com/kornelski/pngquant | SCR_024169 | 2026-08-07 09:30:11 | 0 | |||||||||
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PiGx-RNAseq Resource Report Resource Website |
PiGx-RNAseq (RRID:SCR_024160) | software resource, software toolkit | Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. | reproducible genomics analysis pipelines, GNU Guix, RNA sequencing analysis, chromatin immunoprecipitation sequencing analysis, bisulfite-treated DNA sequencing analysis, single cell resolution RNA sequencing analysis, | is listed by: Debian | PMID:30277498 | Free, Available for download, Freely available, | OMICS_33677 | https://sources.debian.org/src/pigx-rnaseq/ | SCR_024160 | pigx-rnaseq | 2026-08-07 09:30:11 | 0 | ||||||
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picopore Resource Report Resource Website |
picopore (RRID:SCR_024161) | software library, software resource, software toolkit | Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality. | reducing storage size, Oxford Nanopore Technologies datasets, without functionality loss, | is listed by: Debian | PMID:28413619 | Free, Available for download, Freely available, | https://sources.debian.org/src/picopore/ | SCR_024161 | 2026-08-07 09:30:06 | 0 | ||||||||
|
PHYLOViZ Resource Report Resource Website 100+ mentions |
PHYLOViZ (RRID:SCR_024162) | software library, software resource, software toolkit | Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods. | JAVA, phylogenetic inference, data visualization, sequence based typing methods, generate allelic profiles and their associated epidemiological data, | is listed by: Debian | PMID:22568821 | Free, Available for download, Freely available, | https://sources.debian.org/src/phyloviz-core/ | SCR_024162 | 2026-08-07 09:30:11 | 109 | ||||||||
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Change-O Resource Report Resource Website 10+ mentions |
Change-O (RRID:SCR_023986) | software resource, software toolkit | Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences. | processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, reconstructing germline sequences, | is listed by: Debian | PMID:26069265 | Free, Available for download, Freely available | OMICS_08874 | https://sources.debian.org/src/changeo/ | SCR_023986 | changeo | 2026-08-07 09:30:09 | 11 | ||||||
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CDK Resource Report Resource Website 10+ mentions |
CDK (RRID:SCR_023985) | software library, software resource, software toolkit | Open Source software modular Java libraries for cheminformatics. | Java libraries, cheminformatics, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/cdk/ | SCR_023985 | cdk, Chemistry Development Kit | 2026-08-07 09:30:08 | 10 | ||||||||
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ImageTooth Resource Report Resource Website |
ImageTooth (RRID:SCR_024039) | software library, software resource, software toolkit | Software library to generate images for odontograms.Allows to choose between png or jpg images. | generate images for odontograms, generate images, odontograms | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/imagetooth/ | SCR_024039 | imagetooth | 2026-08-07 09:30:09 | 0 | ||||||||
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TaxonomyTree Resource Report Resource Website |
TaxonomyTree (RRID:SCR_024090) | software library, software resource, software toolkit | Software library used by other RDP tools.TaxonomyTree building and traversal utility classes. | RDP tools, taxonomy tree building and traversal utility classes, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/librdp-taxonomy-tree-java/ | SCR_024090 | librdp-taxonomy-tree-java | 2026-08-07 09:30:10 | 0 | ||||||||
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Sort-Key-Top Resource Report Resource Website |
Sort-Key-Top (RRID:SCR_024092) | software library, software resource, software toolkit | Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures. | select the top n elements from a list, custom key extraction procedures, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libsort-key-top-perl/ | SCR_024092 | libsort-key-top-perl, Sort-Key-Top - select and sort top n elements | 2026-08-07 09:30:04 | 0 | ||||||||
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libStatGen Resource Report Resource Website |
libStatGen (RRID:SCR_024093) | software library, software resource, software toolkit | Software library as set of classes for creating statistical genetic programs. | creating statistical genetic programs | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libstatgen/, https://github.com/statgen/libStatGen | SCR_024093 | C++ Library: libStatGen, libstatgen | 2026-08-07 09:30:10 | 0 | ||||||||
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ThreadPool Resource Report Resource Website |
ThreadPool (RRID:SCR_024094) | software library, software resource, software toolkit | Software C++ thread pool library. | C++ thread pool library | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libthread-pool/ | SCR_024094 | Thread pool, libthread-pool | 2026-08-07 09:30:10 | 0 | ||||||||
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OpenCFU Resource Report Resource Website 1+ mentions |
OpenCFU (RRID:SCR_024142) | software library, software resource, software toolkit | Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit. | count cell colonies, enumeration of colony forming unit, | is listed by: Debian | PMID:23457446 | Free, Available for download, Freely available, | OMICS_14951 | https://sources.debian.org/src/opencfu/ | SCR_024142 | opencfu | 2026-08-07 09:30:10 | 5 | ||||||
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GATB Resource Report Resource Website 1+ mentions |
GATB (RRID:SCR_024024) | software resource, software toolkit | Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis. | genome assembly, genome analysis, | is listed by: Debian | PMID:24990603 | Free, Available for download, Freely available | OMICS_04834 | https://sources.debian.org/src/gatb-core/, https://gatb.inria.fr/software/gatb-core/ | SCR_024024 | GATB-CORE, gatb-core, GATB-TOOLS, The Genome Analysis Toolbox with de-Bruijn graph | 2026-08-07 09:30:03 | 4 | ||||||
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BBHash Resource Report Resource Website |
BBHash (RRID:SCR_023972) | software library, software resource, software toolkit | Software library for building minimal perfect hash function. Designed to handle large scale datasets. | hash function library, large scale datasets, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bbhash/ | SCR_023972 | bbhash | 2026-08-07 09:30:08 | 0 | ||||||||
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bambamc Resource Report Resource Website |
bambamc (RRID:SCR_023970) | software resource, software toolkit | Software package contains lightweight C implementation of name collating BAM file input and BAM file output. | C implementation, name collating BAM file input, BAM file output, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/bambamc/ | SCR_023970 | 2026-08-07 09:30:08 | 0 | |||||||||
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Odil Resource Report Resource Website |
Odil (RRID:SCR_024140) | software library, software resource, software toolkit | Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard. | DICOM library, C++11, Python, API, DICOM standard different parts, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/odil/ | SCR_024140 | odil | 2026-08-07 09:30:05 | 0 |
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