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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
https://neobio.sourceforge.net/
Software library of sequence alignment algorithms implemented in Java.
Proper citation: NeoBio (RRID:SCR_024131) 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
https://doua.prabi.fr/software/njplot
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.
Proper citation: NJplot (RRID:SCR_024137) 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://pypi.org/project/OBITools/
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Proper citation: OBITools (RRID:SCR_024141) 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://www.orthanc-server.com/
Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.
Proper citation: Orthanc (RRID:SCR_024145) Copy
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