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https://github.com/jakejh/zeitzeiger
R package for regularized supervised learning on high-dimensional data from an oscillatory system. Zeitzeiger can quantify rhythmic behavior, make accurate predictions, identify major patterns and important features, and detect when the oscillator is perturbed.
Proper citation: Zeitzeiger (RRID:SCR_014791) Copy
http://stat.ethz.ch/R-manual/R-patched/library/stats/html/prcomp.html
R documentation for a function that performs a principal components analysis on a given data matrix and returns the results as an object of class prcomp.
Proper citation: Principal Components Analysis (RRID:SCR_014676) Copy
http://stat.ethz.ch/R-manual/R-devel/library/MASS/html/lda.html
R documentation for a function to perform linear discriminant analysis; specifically, to detect if the within-class covariance matrix is singular.
Proper citation: Linear Discriminant Analysis (RRID:SCR_014675) Copy
http://artiva.gene-networks.net/artiva-2/
Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.
Proper citation: ARTIVA (RRID:SCR_011946) Copy
http://sourceforge.net/projects/adtex/
A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
Proper citation: ADTEx (RRID:SCR_012059) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
http://www.stat.purdue.edu/~doerge/software/TSPM.R
Software using a statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression.
Proper citation: TSPM.R (RRID:SCR_012021) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
https://github.com/sdparekh/zUMIs
Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.
Proper citation: zUMIs (RRID:SCR_016139) Copy
http://zzlab.net/blink/index.html
Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.
Proper citation: BLINK (RRID:SCR_016288) Copy
http://www.bioconductor.org/packages/release/bioc/html/flowCL.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.
Proper citation: flowCL (RRID:SCR_000046) Copy
http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html
Software package for various databases of microRNA Targets.
Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy
https://CRAN.R-project.org/package=NBR
Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models.
Proper citation: Network-Based R-Statistics (RRID:SCR_019114) Copy
A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: PIPE-CLIP (RRID:SCR_005820) Copy
http://www003.upp.so-net.ne.jp/pub/publications.html#sl
Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)
Proper citation: LDGROUP (RRID:SCR_006282) Copy
http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm
Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)
Proper citation: POOLSCORE (RRID:SCR_007514) Copy
https://atgu.mgh.harvard.edu/plinkseq/
An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software)
Proper citation: PLINK/SEQ (RRID:SCR_013193) Copy
https://github.com/mikelove/tximport
Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.
Proper citation: tximport (RRID:SCR_016752) Copy
https://github.com/theislab/scanpy
Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time.
Proper citation: scanpy (RRID:SCR_018139) Copy
https://cran.r-project.org/web/packages/madsim/index.html
A function which allows users to generate two biological conditions synthetic microarray datasets. The user provides a subset of parameters, but default parameter settings can be modified.
Proper citation: madsim (RRID:SCR_014765) Copy
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