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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Lighter Resource Report Resource Website |
Lighter (RRID:SCR_024095) | data analysis software, data processing software, software application, software resource | Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors. | kmer-based error correction method, whole genome sequencing data, correct the reads containing sequence errors, | is listed by: Debian | PMID:25398208 | Free, Available for download, Freely available, | https://sources.debian.org/src/lighter/ | SCR_024095 | lighter | 2026-09-05 06:30:29 | 0 | |||||||
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Brainways Resource Report Resource Website 1+ mentions |
Brainways (RRID:SCR_024402) | data processing software, image analysis software, software application, software resource | Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices. | OpenBehavior, slice quantification, register coronal slices, quantify fluorescent markers, slice matching to atlas, registration and analysis of fluorescent markers, coronal brain slices, | is listed by: OpenBehavior | DOI:10.1101/2023.05.25.542252 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/brainways/ | SCR_024402 | 2026-09-05 06:30:30 | 1 | ||||||||
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RiboToolkit Resource Report Resource Website 1+ mentions |
RiboToolkit (RRID:SCR_024406) | data access protocol, software resource, web service | Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. | Ribo-seq data analysis, analysis and annotation of ribosome profiling data, decode mRNA translation at codon resolution, data cleaning and quality evaluation, | NCI R35 CA232115 | PMID:32427338 | Free, Freely available | SCR_024406 | 2026-09-05 06:30:30 | 2 | |||||||||
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ramr Resource Report Resource Website |
ramr (RRID:SCR_024408) | data analysis software, data processing software, software application, software resource | Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms. | rare aberrantly methylated regions, low frequency aberrant methylation events detection, visualize found aberrantly methylated regions, | K.G. Jebsen foundation ; Norwegian Cancer Society ; Norwegian Health Region West ; Norwegian Research Council |
PMID:34383893 | Free, Available for download, Freely available | https://github.com/BBCG/ramr | SCR_024408 | rare aberrantly methylated regions | 2026-09-05 06:30:30 | 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 | 2026-09-05 06:30:30 | 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 | 2026-09-05 06:30:30 | 0 | ||||||||
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Tn-seq explorer Resource Report Resource Website 1+ mentions |
Tn-seq explorer (RRID:SCR_024387) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:30 | 3 | |||||||
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PyWavelets Resource Report Resource Website 10+ mentions |
PyWavelets (RRID:SCR_024421) | data analysis software, data processing software, software application, software resource | Software Python package for wavelet analysis. | Python, wavelet analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024421 | 2026-09-05 06:30:30 | 17 | ||||||||||
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TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_024389) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:30 | 1 | ||||||
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TREE-PUZZLE Resource Report Resource Website 1+ mentions |
TREE-PUZZLE (RRID:SCR_024382) | data analysis software, data processing software, software application, software resource | Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set. | reconstruct phylogenetic trees, molecular sequence data, maximum likelihood, compute pairwise maximum likelihood distances, conduct statistical tests, data analysis, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_18458 | https://sources.debian.org/src/tree-puzzle/ | https://sources.debian.org/src/tree-ppuzzle/ | SCR_024382 | tree-puzzle | 2026-09-05 06:30:30 | 4 | ||||||
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NORSp Resource Report Resource Website |
NORSp (RRID:SCR_024139) | data access protocol, simulation software, software application, software resource, web service | 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 | 2026-09-05 06:30:29 | 0 | |||||||
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ProteinPilot Resource Report Resource Website 100+ mentions |
ProteinPilot (RRID:SCR_024414) | data analysis software, data processing software, software application, software resource | Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems. | protein identification, protein expression analysis, post translational modification search, | is listed by: SoftCite | Restricted | https://sciex.com/content/dam/SCIEX/pdf/posters/ProteinPilot-Software-Overview.pdf | SCR_024414 | 2026-09-05 06:30:30 | 265 | |||||||||
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pRRophetic Resource Report Resource Website 10+ mentions |
pRRophetic (RRID:SCR_024417) | simulation software, software application, software resource | Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data, | clinical chemotherapeutic response prediction, tumor gene expression levels, predict phenotypes, | is listed by: SoftCite | U01GM61393 ; GM089941 ; CA139278 ; University of Chicago ; UL1RR024999 |
PMID:25229481 | Free, Available for download, Freely available | SCR_024417 | 2026-09-05 06:30:30 | 33 | ||||||||
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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 | 2026-09-05 06:30:29 | 0 | |||||||
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Edlib Resource Report Resource Website 1+ mentions |
Edlib (RRID:SCR_024078) | alignment software, data processing software, image analysis software, software application, software resource | 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. | 2026-09-05 06:30:29 | 2 | |||||||
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metaBIT Resource Report Resource Website |
metaBIT (RRID:SCR_024111) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:29 | 0 | |||||||
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qtlreaper Resource Report Resource Website |
qtlreaper (RRID:SCR_024199) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:29 | 0 | |||||||||
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MHAP Resource Report Resource Website |
MHAP (RRID:SCR_024113) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:29 | 0 | ||||||
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MindTheGap Resource Report Resource Website 1+ mentions |
MindTheGap (RRID:SCR_024115) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:29 | 3 | |||||||
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MafFilter Resource Report Resource Website 10+ mentions |
MafFilter (RRID:SCR_024105) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:29 | 12 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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