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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pssh2 Resource Report Resource Website |
pssh2 (RRID:SCR_024181) | software toolkit, software library, software resource | Software tools for creating the sequence-to-structure alignment database PSSH2. | creating sequence-to-structure alignment database, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pssh2/ | SCR_024181 | 2026-08-05 10:47:59 | 0 | |||||||||
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pyepl Resource Report Resource Website 1+ mentions |
pyepl (RRID:SCR_024182) | software toolkit, software library, software resource | Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses. | coding psychology experiments, Python | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/python-pyepl/ | SCR_024182 | Python Experiment-Programming Library | 2026-08-05 10:47:59 | 3 | ||||||||
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pbcopper Resource Report Resource Website |
pbcopper (RRID:SCR_024152) | software toolkit, software library, software resource | Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications. | data structures, algorithms, utilities for PacBio C++ applications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pbcopper/ | SCR_024152 | 2026-08-05 10:47:59 | 0 | |||||||||
|
Parsnp Resource Report Resource Website 10+ mentions |
Parsnp (RRID:SCR_024153) | software toolkit, software library, 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 | 2026-08-05 10:47:59 | 39 | ||||||
|
epibasix Resource Report Resource Website |
epibasix (RRID:SCR_024275) | software toolkit, software resource | Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement. | epidemiological problems analysis, sample size estimation, contingency table analysis, basic measures of agreement, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-epibasix/ | SCR_024275 | epibasix: Elementary Epidemiological Functions for Epidemiology and Biostatistics, r-cran-epibasix | 2026-08-05 10:48:02 | 0 | ||||||||
|
PDB2PQR Resource Report Resource Website 1+ mentions |
PDB2PQR (RRID:SCR_024155) | software toolkit, software library, 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 | 2026-08-05 10:47:59 | 2 | ||||||
|
PfTools Resource Report Resource Website 1+ mentions |
PfTools (RRID:SCR_024158) | software toolkit, software library, 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 | 2026-08-05 10:47:59 | 2 | |||||||
|
PhySamp Resource Report Resource Website 1+ mentions |
PhySamp (RRID:SCR_024159) | software toolkit, software library, 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 | 2026-08-05 10:47:59 | 1 | ||||||
|
biwt Resource Report Resource Website |
biwt (RRID:SCR_024271) | software toolkit, software resource | Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator. | compute multivariate location, scale and correlation estimates, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-biwt/ | SCR_024271 | biwt: Compute the Biweight Mean Vector and Covariance & Correlation Matrice, r-cran-biwt | 2026-08-05 10:48:01 | 0 | ||||||||
|
Epi Resource Report Resource Website 1+ mentions |
Epi (RRID:SCR_024272) | software toolkit, software resource | Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets. | demographic and epidemiological analysis in Lexis diagram, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-epi/ | SCR_024272 | r-cran-epi, Epi: Statistical Analysis in Epidemiology | 2026-08-05 10:48:02 | 1 | ||||||||
|
ParsInsert Resource Report Resource Website |
ParsInsert (RRID:SCR_024163) | software toolkit, software library, software resource | Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. | Parsimonious Insertion, unclassified sequences, phylogenetic tree, produce phylogenetic tree, produce taxonomic classification, produce sequences, microbial community sequence analysis, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21460 | https://sources.debian.org/src/parsinsert/ | SCR_024163 | parsinsert | 2026-08-05 10:47:59 | 0 | |||||||
|
python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software toolkit, software library, software resource | Software Python library and associated set of scripts for rapid implementation of genome scale analyses. | rapid implementation of genome scale analyses, | is listed by: Debian | OMICS_18239 | https://sources.debian.org/src/python3-bx/ | SCR_024202 | 2026-08-05 10:47:59 | 24 | |||||||||
|
Murasaki Resource Report Resource Website |
Murasaki (RRID:SCR_024132) | software toolkit, software library, software resource | Software language-theory based homology detection tool across multiple large genomes. | language-theory based homology detection, multiple large genomes, | is listed by: Debian | PMID:20885980 | Free, Available for download, Freely available, | OMICS_11714 | https://sources.debian.org/src/murasaki/ | SCR_024132 | murasaki | 2026-08-05 10:47:58 | 0 | ||||||
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preprocesscore Resource Report Resource Website 50+ mentions |
preprocesscore (RRID:SCR_024254) | software toolkit, software resource | Software library of core preprocessing routines. | core preprocessing routines, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-preprocesscore/ | SCR_024254 | 2026-08-05 10:48:01 | 57 | |||||||||
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qusage Resource Report Resource Website 1+ mentions |
qusage (RRID:SCR_024255) | software toolkit, software resource | Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies. | test for gene expression studies, | is listed by: Debian | PMID:23921631 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-qusage/ | SCR_024255 | Quantitative Set Analysis for Gene Expression | 2026-08-05 10:48:00 | 3 | |||||||
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Entrez Direct Resource Report Resource Website 1+ mentions |
Entrez Direct (RRID:SCR_024136) | software toolkit, software library, 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 | 2026-08-05 10:47:58 | 9 | |||||||||
|
rsamtools Resource Report Resource Website 50+ mentions |
rsamtools (RRID:SCR_024257) | software toolkit, software resource | Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files. | tabix interface, samtools interface, bcftools interface, Sequence Alignment Map manipulation, SAM manipulation, FASTA manipulation, binary variant call manipulation, compressed indexed tab delimited files manipulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rsamtools/ | SCR_024257 | 2026-08-05 10:48:01 | 58 | |||||||||
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NJplot Resource Report Resource Website 1+ mentions |
NJplot (RRID:SCR_024137) | software toolkit, software library, 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 | 2026-08-05 10:47:58 | 2 | |||||||
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savr Resource Report Resource Website |
savr (RRID:SCR_024258) | software toolkit, software resource | Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots. | parse Illumina Sequence Analysis Viewer files, access data, generate QC plots, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15992 | https://sources.debian.org/src/r-bioc-savr/ | SCR_024258 | 2026-08-05 10:48:00 | 0 | ||||||||
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nanostringqcpro Resource Report Resource Website 1+ mentions |
nanostringqcpro (RRID:SCR_024250) | software toolkit, software resource | Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output. | assess quality of NanoString mRNA gene expression data, identify outlier probes and outlier samples, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-nanostringqcpro/ | SCR_024250 | 2026-08-05 10:48:00 | 7 |
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