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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/incidence/index.html

Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats.

Proper citation: incidence (RRID:SCR_024276) Copy   

•   Source: SciCrunch Registry

https://github.com/sib-swiss/pftools3

Software suite of tools to build and search generalized profiles.

Proper citation: PfTools (RRID:SCR_024158) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/genetics/index.html

Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium.

Proper citation: genetics (RRID:SCR_024279) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/dynamicTreeCut/index.html

Software R package contains methods for detection of clusters in hierarchical clustering dendrograms.

Proper citation: dynamicTreeCut (RRID:SCR_024280) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/preprocessCore/

Software library of core preprocessing routines.

Proper citation: preprocesscore (RRID:SCR_024254) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/savR/

Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots.

Proper citation: savr (RRID:SCR_024258) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/NanoStringQCPro/

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.

Proper citation: nanostringqcpro (RRID:SCR_024250) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/PWMEnrich/

Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation.

Proper citation: pwmenrich (RRID:SCR_024249) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/XVector/

Software R package provides memory efficient S4 classes for storing sequences externally.

Proper citation: xvector (RRID:SCR_024263) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/BoolNet/index.html

Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks.

Proper citation: BoolNet (RRID:SCR_024264) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/cmprsk/index.html

Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks.

Proper citation: cmprsk (RRID:SCR_024265) Copy   

•   Source: SciCrunch Registry