Open Source S/R Software - Page 5

We have moved, the project is now at http://distancesampling.org

Django-dataplot enables developers using the Django web framework to seamlessly integrate data-driven graphical plots into their web pages.

DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.

A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.

Enrichment analysis for customized organisms

EDDA is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance. EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. More details of EDDA can be found at Luo, Huaien et al. “The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” Genome Biology 2014;15(12):527 (http://www.ncbi.nlm.nih.gov/pubmed/25517037/). An accompanying web server (http://edda.gis.a-star.edu.sg/) is available for easy access to some functionality of EDDA. Additionally a Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/EDDA.html) is available for easy installation of EDDA R package.

My goal is a library for R (www.r-project.org) which encodes concepts relevant to statistical analysis in ecology in relatively easy scalable functions. Includes hierarchical scaling of predictors, density calculations, lme4 model sets, etc...

EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be utilized for any -omic platform. We have shown its utility in LC-MS/MS and metabolomics in the following two papers: 1) PMID: 19602524. "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition". Karpievitch YV, Taverner T, Adkins JN, Callister SJ, Anderson GA, Smith RD, Dabney AR. Bioinformatics 2009 2) "Metabolomics data normalization with EigenMS" Karpievitch YV, Nikolic SB, Wilson R, Sharman JE, Edwards LM. PLoS One 2014

Set of tools for basic analysis of electrophysiological data. The Python classes show how to call OpenElectrophy functions and save data. The R library applies circular statistics to spike phase data and saves the best von Mises fit and the Rayleigh statistics on the disk. The wavelet coherence analysis is done in R by the package "sowas". Check the module R_coherence to see how we solved that problem. This packages may be useful for people who start using OpenElectrophy and circular statistics in R. If you find errors, please report them. The project is still in development, so in the future you'll get updates.

ElicitN uses R and a tcltk gui interface for eliciting a number from an appropriate expert. The code has been modified from it's original version designed specifically for eliciting the number of species on coral reefs from expert taxonomists. For more information please refer to: http://dx.doi.org/10.1016/j.envsoft.2011.11.011 Please also refer to GitHub for a even simpler more recently maintained version of the project: https://github.com/beckyfisher/ElicitN

EnvStats is an R package for environmental statistics. It is the open-source successor to the commercial module for S-Plus© called "EnvironmentalStats for S-Plus", which was first released in April, 1997. The EnvStats package, along with the R software environment, provides comprehensive and powerful software for environmental data analysis. EnvStats brings the major environmental statistical methods found in the literature and regulatory guidance documents into one statistical package, along with an extensive hypertext help system that explains what these methods do, how to use these methods, and where to find them in the environmental statistics literature. Also included are numerous built-in data sets from regulatory guidance documents and the environmental statistics literature. EnvStats combined with other R packages (e.g., for spatial analysis) provides the environmental scientist, statistician, researcher, and technician with tools to “get the job done!”

Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.

Excelsi-R is an Excel add-in that allows Excel spreadsheets to harness the power of the R statistical language by connecting to a running R process. R does not need to be installed on the computer running Excel, but it does require access to an R instance running Rserve (which can be on a remote computer). It supports incorporating R plots and graphs in an Excel workbook.

Open, extensible web-based collaborative platform for microarray gene expression, sequence and PPI data analysis, exposing distinct chainable components for clustering, pattern discovery, statistics (thru R), machine-learning algorithms and visualization

An R package that performs forward-backward fragment assembling segmentation. Reference: BMC Bioinformatics. 2007 May 3;8:145.

FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases.

FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.

GEOSS (Gene Expression Open Source System), formerly known as GeneX Va, provides a web-based interface for the storage and analysis of Affymetrix GeneChipŽ and other microarray data. It has been developed by engineers at the GeneChip/Microarray Bioinform

GNUexp is a GNUstep/Cocoa framework and a collection of tools helping you to plan, develop, and administer applications associated with visual psychophysics, experimental psychology and statistical data analysis.

GenCart: Genome Cartology in the R Statistical Programming Language

Hoea is a python module for hierarchical ontology enrichment analysis, which facilitated GO (Gene Ontology)/KO (KEGG Orthology) enrichment analysis at any desktop.

The current software contains the implementation for the 454 pyrosequencing platform.

This package, for R environment, detects DAE peaks ratio on data gotten from LightCycler instrument.