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https://bioconductor.org/packages/release/bioc/html/annotate.html
Software R package for using R enviroments for annotation.
Proper citation: annotate (RRID:SCR_024221) Copy
https://bioconductor.org/packages/release/bioc/html/affyio.html
Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats.
Proper citation: affyio (RRID:SCR_024223) Copy
https://bioconductor.org/packages/release/bioc/html/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) Copy
https://github.com/aschafu/PSSH2
Software tools for creating the sequence-to-structure alignment database PSSH2.
Proper citation: pssh2 (RRID:SCR_024181) Copy
https://pyepl.sourceforge.net/
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.
Proper citation: pyepl (RRID:SCR_024182) Copy
https://github.com/PacificBiosciences/pbcopper
Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications.
Proper citation: pbcopper (RRID:SCR_024152) Copy
https://harvest.readthedocs.io/en/latest/content/parsnp.html
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.
Proper citation: Parsnp (RRID:SCR_024153) Copy
https://cran.r-project.org/web/packages/epibasix/index.html
Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement.
Proper citation: epibasix (RRID:SCR_024275) Copy
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
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.
Proper citation: PDB2PQR (RRID:SCR_024155) Copy
https://github.com/sib-swiss/pftools3
Software suite of tools to build and search generalized profiles.
Proper citation: PfTools (RRID:SCR_024158) Copy
https://jydu.github.io/physamp/
Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree.
Proper citation: PhySamp (RRID:SCR_024159) Copy
https://cran.r-project.org/web/packages/biwt/index.html
Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator.
Proper citation: biwt (RRID:SCR_024271) Copy
https://cran.r-project.org/web/packages/Epi/index.html
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.
Proper citation: Epi (RRID:SCR_024272) Copy
https://sourceforge.net/projects/parsinsert/
Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis.
Proper citation: ParsInsert (RRID:SCR_024163) Copy
https://github.com/bxlab/bx-python
Software Python library and associated set of scripts for rapid implementation of genome scale analyses.
Proper citation: python-bx (RRID:SCR_024202) Copy
http://murasaki.dna.bio.keio.ac.jp/wiki/
Software language-theory based homology detection tool across multiple large genomes.
Proper citation: Murasaki (RRID:SCR_024132) Copy
https://bioconductor.org/packages/preprocessCore/
Software library of core preprocessing routines.
Proper citation: preprocesscore (RRID:SCR_024254) Copy
https://bioconductor.org/packages/qusage/
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.
Proper citation: qusage (RRID:SCR_024255) Copy
https://www.ncbi.nlm.nih.gov/books/NBK179288/
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.
Proper citation: Entrez Direct (RRID:SCR_024136) Copy
https://bioconductor.org/packages/Rsamtools/
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.
Proper citation: rsamtools (RRID:SCR_024257) Copy
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