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https://cme.h-its.org/exelixis/web/software/exabayes/
Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters.
Proper citation: ExaBayes (RRID:SCR_024019) Copy
Software to support biomedical image computing.
Proper citation: CTK (RRID:SCR_024002) Copy
https://github.com/a-slide/pycoQC
Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data.
Proper citation: pycoqc (RRID:SCR_024185) Copy
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/altcdfenvs.html
Software R package contains convenience data structures and functions to handle cdfenvs.
Proper citation: altcdfenvs (RRID:SCR_024225) 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://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
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://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://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
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
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
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
https://bioconductor.org/packages/XVector/
Software R package provides memory efficient S4 classes for storing sequences externally.
Proper citation: xvector (RRID:SCR_024263) Copy
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
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
https://cran.r-project.org/web/packages/bio3d/index.html
Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data.
Proper citation: bio3d (RRID:SCR_024266) Copy
https://cran.r-project.org/web/packages/DoseFinding/index.html
Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology.
Proper citation: DoseFinding (RRID:SCR_024268) Copy
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