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http://www.nitrc.org/projects/rfmri/

The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.

Proper citation: R-package for adaptive fMRI analysis (RRID:SCR_002530) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

https://github.com/acnash/CPRD_Additional_Clinical/blob/master/CPRDLooksups.R

Software R tool used to identify and retrieve CPRD clinical additional record information such as, smoking, weight/BMI, and medical tests.

Proper citation: CPRDLooksups.R (RRID:SCR_018959) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iontree.html

Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Proper citation: iontree (RRID:SCR_002813) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/fastcluster/1.2.3/

Software Python library for hierarchical clustering. Fast Hierarchical, Agglomerative Clustering Routines for R and Python.

Proper citation: fastcluster (RRID:SCR_023597) Copy   

•   Source: SciCrunch Registry

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

An R package which contains functions for validating the results of a clustering analysis.

Proper citation: clValid (RRID:SCR_014626) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/ggplot2/index.html

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Proper citation: ggplot2 (RRID:SCR_014601) Copy   

•   Source: SciCrunch Registry

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

An R-package which uses Object Oriented Data Analysis (OODA) methods to analyze taxonomic trees directly, providing tools to model, compare, and visualize populations of taxonomic tree objects.

Proper citation: HMPTrees (RRID:SCR_014613) Copy   

•   Source: SciCrunch Registry

https://github.com/dgrapov/CTSgetR

R interface to Chemical Translation Service which provides translation between chemical and biological database identifiers.

Proper citation: CTSgetR (RRID:SCR_014672) Copy   

•   Source: SciCrunch Registry

https://rdocumentation.org/packages/survminer/versions/0.4.9

Software R package provides functions for facilitating survival analysis and visualization.

Proper citation: survminer (RRID:SCR_021094) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=rstatix

Software R package for basic statistical tests including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. Output of each test is automatically transformed into data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate analysis of factorial experiments. Can compute several effect size metrics.Package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.

Proper citation: rstatix (RRID:SCR_021240) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/cob87icW6z/cafe/wiki/Home

R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Proper citation: CAFE (RRID:SCR_005983) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/RUVSeq.html

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

Proper citation: RUVSeq (RRID:SCR_006263) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

•   Source: SciCrunch Registry

http://www.jstatsoft.org/v49/i08/.

Data Analysis GUI for R. The program is based on Java's Swing GUI library and includes an Excel-like spreadsheet for easy data viewing and editing.

Proper citation: R package: Deducer (RRID:SCR_015659) Copy   

•   Source: SciCrunch Registry

https://github.com/ChristofSeiler/braincog

Software package to elucidate complex interactions between subsets of neuroanatomical features and subsets of cognitive features. briancog specializes in differential correlation analysis.

Proper citation: braincog (RRID:SCR_015871) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scater.html

Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data.

Proper citation: scater (RRID:SCR_015954) Copy   

•   Source: SciCrunch Registry

https://www.jamovi.org/

Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience.

Proper citation: jamovi (RRID:SCR_016142) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/recount/

RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Proper citation: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) Copy   

•   Source: SciCrunch Registry