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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Filtlong Resource Report Resource Website 100+ mentions |
Filtlong (RRID:SCR_024020) | data processing software, software application, software resource | Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter. | filtering long reads by quality, read length, read identity, filtering reads, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/filtlong/ | SCR_024020 | filtlong | 2026-08-04 09:45:23 | 309 | ||||||||
|
NORSp Resource Report Resource Website |
NORSp (RRID:SCR_024139) | simulation software, web service, software resource, data access protocol, software application | Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions. | NOn-Regular Secondary Structure, predict disordered regions in protein, predict long regions with no regular secondary structure, protein sequence, protein secondary structure analysis, transmembrane helices and coiled-coil analysis, presence and position of disordered regions, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21452 | https://sources.debian.org/src/norsp/ | SCR_024139 | , NORSp - predictor of NOn-Regular Secondary Structure, norsp, NOn-Regular Secondary Structure predictor | 2026-08-04 09:45:25 | 0 | |||||||
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Metastudent Resource Report Resource Website |
Metastudent (RRID:SCR_024110) | simulation software, software application, software resource | Software tool to predict gene ontology terms for protein sequences through homology. | predict gene ontology terms, protein sequences, through homology, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20187 | https://sources.debian.org/src/metastudent/, https://sources.debian.org/src/metastudent-data/ | SCR_024110 | metastudent-data, metastudent | 2026-08-04 09:45:26 | 0 | |||||||
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Edlib Resource Report Resource Website 1+ mentions |
Edlib (RRID:SCR_024078) | data processing software, alignment software, software resource, software application, image analysis software | Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance. | sequence alignment, edit Levenshtein distance. | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15611 | https://sources.debian.org/src/libedlib/, http://martinsos.github.io/edlib/ | SCR_024078 | libedlib, Edib: A lightweight and super fast C/C++ library for sequence alignment using edit distance. | 2026-08-04 09:45:24 | 1 | |||||||
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metaBIT Resource Report Resource Website |
metaBIT (RRID:SCR_024111) | data processing software, software application, software resource, data analysis software | Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing. | metagenomic and taxonomical analysis, shotgun sequencing, | is listed by: Debian | PMID:27238636 | Free, Available for download, Freely available, | https://sources.debian.org/src/metabit/ | SCR_024111 | metabit | 2026-08-04 09:45:26 | 0 | |||||||
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qtlreaper Resource Report Resource Website |
qtlreaper (RRID:SCR_024199) | data processing software, software application, software resource, data analysis software | Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL. | rapidly scanning microarray expression data for QTLs, association between each expression trait and all genotypes, estimate confidence region for location of putative QTL, Quantitative Trait Loci, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/qtlreaper/ | SCR_024199 | 2026-08-04 09:45:27 | 0 | |||||||||
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MHAP Resource Report Resource Website |
MHAP (RRID:SCR_024113) | data processing software, software application, software resource, data analysis software | Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data. | detect overlaps between noisy long-read sequence data, probabilistic sequence overlapping algorithm, | is listed by: Debian | PMID:26006009 | Free, Available for download, Freely available, | OMICS_13515 | https://sources.debian.org/src/mhap/, https://github.com/marbl/MHAP | SCR_024113 | MinHash Alignment Process, mhap | 2026-08-04 09:45:26 | 0 | ||||||
|
MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | data processing software, software application, software resource, data analysis software | Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. | perform detection and assembly of DNA insertion variants, NGS read datasets, reference genome, call insertions, donor genome, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_05472 | https://sources.debian.org/src/mindthegap/ | SCR_024115 | mindthegap | 2026-08-04 09:45:25 | 3 | |||||||
|
MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | data processing software, software application, software resource, data analysis software | Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc. | genome alignments analysis, parse and manipulate MAF files, genome alignment processor, | is listed by: Debian | PMID:24447531 | Free, Available for download, Freely available, | OMICS_06743 | https://sources.debian.org/src/maffilter/, https://github.com/jydu/maffilter | SCR_024105 | MafFilter a genome alignment processor, maffilter | 2026-08-04 09:45:26 | 11 | ||||||
|
sparta Resource Report Resource Website 1+ mentions |
sparta (RRID:SCR_024349) | data processing software, software application, software resource, data analysis software | Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms. | analyzing single-end Illumina RNA-seq data, | is listed by: Debian | PMID:26847232 | Free, Available for download, Freely available, | https://sources.debian.org/src/sparta/ | SCR_024349 | SPARTA | 2026-08-04 09:45:30 | 9 | |||||||
|
Maude Resource Report Resource Website |
Maude (RRID:SCR_024108) | portal, software resource, software library, project portal, software toolkit, data or information resource | Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation. | equational and rewriting logic specification and programming, equational specification and programming, rewriting logic computation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/maude/, http://maude.cs.illinois.edu/w/index.php/Maude_download_and_installation | SCR_024108 | Maude, maude | 2026-08-04 09:45:26 | 0 | ||||||||
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mPTP Resource Report Resource Website 1+ mentions |
mPTP (RRID:SCR_024121) | data processing software, software application, software resource, data analysis software | Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets. | single locus species delimitation, ML delimitation from inferred phylogenetic tree of the samples, ML delimitation, inferred phylogenetic tree, samples inferred phylogenetic tree, | is listed by: Debian | PMID:28108445 | Free, Available for download, Freely available, | OMICS_15264 | https://sources.debian.org/src/mptp/ | SCR_024121 | , mptp, multi-rate Poisson Tree Processes | 2026-08-04 09:45:25 | 1 | ||||||
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Molekel Resource Report Resource Website 1+ mentions |
Molekel (RRID:SCR_024122) | data processing software, data visualization software, software application, software resource | Open source multi platform molecular visualization program. | molecular visualization | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/molekel/ | SCR_024122 | molekel | 2026-08-04 09:45:27 | 1 | ||||||||
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MRtrix3 Resource Report Resource Website 100+ mentions |
MRtrix3 (RRID:SCR_024123) | data processing software, software application, software resource, data analysis software | Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. | diffusion MRI analyses, tractography, next generation group level analyses, | is listed by: Debian | PMID:31473352 | Free, Available for download, Freely available, | https://sources.debian.org/src/mrtrix3/ | SCR_024123 | mrtrix3 | 2026-08-04 09:45:26 | 185 | |||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | simulation software, software application, software resource | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-08-04 09:45:24 | 0 | ||||||||
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MIA Resource Report Resource Website |
MIA (RRID:SCR_024081) | data processing software, software application, software resource, image analysis software | Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality. | gray scale medical image analysis, interactive image processing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/mia/ | https://sources.debian.org/src/libmialm/ | SCR_024081 | python3-mia, libmia-2.4-dev, mia-tools, mia-viewit, libvistaio-dev, libmialm-dev, libmiaviewit-dev, libmialm, mialmpick | 2026-08-04 09:45:24 | 0 | |||||||
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toppred Resource Report Resource Website 1+ mentions |
toppred (RRID:SCR_024385) | simulation software, software application, software resource | Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins. | Membrane protein structure prediction, transmembrane topology prediction, predicting topology, bacterial inner membrane proteins topology prediction, | is listed by: Debian | PMID:1593632 | Free, Available for download, Freely available, | OMICS_07268 | https://sources.debian.org/src/toppred/ | SCR_024385 | 2026-08-04 09:45:30 | 3 | |||||||
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trace2dbEST Resource Report Resource Website |
trace2dbEST (RRID:SCR_024386) | data processing software, software application, software resource | Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST. | process raw sequenceing chromatograph trace files, file process from EST projects into quality checked sequences, files ready for submission to dbEST, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_33039 | https://sources.debian.org/src/trace2dbest/ | SCR_024386 | 2026-08-04 09:45:31 | 0 | ||||||||
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Tn-seq explorer Resource Report Resource Website 1+ mentions |
Tn-seq explorer (RRID:SCR_024387) | data processing software, software application, software resource, data analysis software | Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions. | high-throughput sequencing data analysis, transposon mutant libraries, read alignment and gene annotation, identify genes, low counts of transposon insertions genes, | is listed by: Debian | PMID:25938432 | Free, Available for download, Freely available, | https://sources.debian.org/src/tn-seqexplorer/ | SCR_024387 | , Tn-seq Explorer, tn-seqexplorer | 2026-08-04 09:45:31 | 3 | |||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_024389) | data processing software, software application, software resource, data analysis software | Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions. | Himar1 TnSeq data analysis, identifying essential genes in individual datasets, comparative analysis between conditions, | is listed by: Debian | PMID:26447887 | Free, Available for download, Freely available, | OMICS_10215 | https://sources.debian.org/src/tnseq-transit/ | SCR_024389 | tnseq-transit | 2026-08-04 09:45:31 | 1 |
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