Showing 29 of total 29 results (show query)
spedygiorgio
markovchain:Easy Handling Discrete Time Markov Chains
Functions and S4 methods to create and manage discrete time Markov chains more easily. In addition functions to perform statistical (fitting and drawing random variates) and probabilistic (analysis of their structural proprieties) analysis are provided. See Spedicato (2017) <doi:10.32614/RJ-2017-036>. Some functions for continuous times Markov chains depend on the suggested ctmcd package.
Maintained by Giorgio Alfredo Spedicato. Last updated 5 months ago.
ctmcdtmcmarkov-chainmarkov-modelr-programmingrcppopenblascpp
104 stars 12.78 score 712 scripts 4 dependents
bioc
PharmacoGx:Analysis of Large-Scale Pharmacogenomic Data
Contains a set of functions to perform large-scale analysis of pharmaco-genomic data. These include the PharmacoSet object for storing the results of pharmacogenomic experiments, as well as a number of functions for computing common summaries of drug-dose response and correlating them with the molecular features in a cancer cell-line.
Maintained by Benjamin Haibe-Kains. Last updated 3 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftwareclassificationdatasetspharmacogenomicpharmacogxcpp
68 stars 11.39 score 442 scripts 3 dependents
crunch-io
crunch:Crunch.io Data Tools
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
Maintained by Greg Freedman Ellis. Last updated 8 days ago.
9 stars 10.47 score 200 scripts 2 dependents
daattali
ddpcr:Analysis and Visualization of Droplet Digital PCR in R and on the Web
An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.
Maintained by Dean Attali. Last updated 1 years ago.
61 stars 9.54 score 131 scripts 2 dependentsbioc
GenomicInteractions:Utilities for handling genomic interaction data
Utilities for handling genomic interaction data such as ChIA-PET or Hi-C, annotating genomic features with interaction information, and producing plots and summary statistics.
Maintained by Liz Ing-Simmons. Last updated 5 months ago.
softwareinfrastructuredataimportdatarepresentationhic
7 stars 9.31 score 162 scripts 5 dependents
flr
FLCore:Core Package of FLR, Fisheries Modelling in R
Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.
Maintained by Iago Mosqueira. Last updated 9 days ago.
fisheriesflrfisheries-modelling
16 stars 8.78 score 956 scripts 23 dependents
r-forge
distr:Object Oriented Implementation of Distributions
S4-classes and methods for distributions.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
8.77 score 327 scripts 32 dependents
magnusdv
pedtools:Creating and Working with Pedigrees and Marker Data
A comprehensive collection of tools for creating, manipulating and visualising pedigrees and genetic marker data. Pedigrees can be read from text files or created on the fly with built-in functions. A range of utilities enable modifications like adding or removing individuals, breaking loops, and merging pedigrees. An online tool for creating pedigrees interactively, based on 'pedtools', is available at <https://magnusdv.shinyapps.io/quickped>. 'pedtools' is the hub of the 'pedsuite', a collection of packages for pedigree analysis. A detailed presentation of the 'pedsuite' is given in the book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
Maintained by Magnus Dehli Vigeland. Last updated 11 days ago.
25 stars 8.72 score 60 scripts 18 dependentsbioc
FRASER:Find RAre Splicing Events in RNA-Seq Data
Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.
Maintained by Christian Mertes. Last updated 5 months ago.
rnaseqalternativesplicingsequencingsoftwaregeneticscoverageaberrant-splicingdiagnosticsoutlier-detectionrare-diseaserna-seqsplicingopenblascpp
41 stars 8.50 score 155 scripts
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
syncrosim
rsyncrosim:The R Interface to 'SyncroSim'
'SyncroSim' is a generalized framework for managing scenario-based datasets (<https://syncrosim.com/>). 'rsyncrosim' provides an interface to 'SyncroSim'. Simulation models can be added to 'SyncroSim' in order to transform these datasets, taking advantage of general features such as defining scenarios of model inputs, running Monte Carlo simulations, and summarizing model outputs. 'rsyncrosim' requires 'SyncroSim' 2.3.5 or higher (API documentation: <https://docs.syncrosim.com/>).
Maintained by Katie Birchard. Last updated 22 days ago.
9 stars 7.09 score 189 scriptsr-forge
distrEx:Extensions of Package 'distr'
Extends package 'distr' by functionals, distances, and conditional distributions.
Maintained by Matthias Kohl. Last updated 2 months ago.
6.64 score 107 scripts 17 dependentsr-forge
distrMod:Object Oriented Implementation of Probability Models
Implements S4 classes for probability models based on packages 'distr' and 'distrEx'.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
6.60 score 139 scripts 6 dependentsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.36 score 63 scripts 6 dependentsbioc
qcmetrics:A Framework for Quality Control
The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.
Maintained by Laurent Gatto. Last updated 5 months ago.
immunooncologysoftwarequalitycontrolproteomicsmicroarraymassspectrometryvisualizationreportwriting
2 stars 6.03 score 2 dependents
albertofranzin
bnstruct:Bayesian Network Structure Learning from Data with Missing Values
Bayesian Network Structure Learning from Data with Missing Values. The package implements the Silander-Myllymaki complete search, the Max-Min Parents-and-Children, the Hill-Climbing, the Max-Min Hill-climbing heuristic searches, and the Structural Expectation-Maximization algorithm. Available scoring functions are BDeu, AIC, BIC. The package also implements methods for generating and using bootstrap samples, imputed data, inference.
Maintained by Alberto Franzin. Last updated 1 years ago.
1 stars 5.40 score 111 scripts 3 dependents
lbbe-software
MareyMap:Estimation of Meiotic Recombination Rates Using Marey Maps
Local recombination rates are graphically estimated across a genome using Marey maps.
Maintained by Aurélie Siberchicot. Last updated 26 days ago.
1 stars 5.30 score 20 scripts
alphaprime7
normfluodbf:Cleans and Normalizes FLUOstar DBF and DAT Files from 'Liposome' Flux Assays
Cleans and Normalizes FLUOstar DBF and DAT Files obtained from liposome flux assays. Users should verify extended usage of the package on files from other assay types.
Maintained by Tingwei Adeck. Last updated 5 months ago.
1 stars 4.98 score 12 scriptsr-forge
RobAStBase:Robust Asymptotic Statistics
Base S4-classes and functions for robust asymptotic statistics.
Maintained by Matthias Kohl. Last updated 2 months ago.
4.96 score 64 scripts 4 dependentsbioc
rsbml:R support for SBML, using libsbml
Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.
Maintained by Michael Lawrence. Last updated 1 months ago.
graphandnetworkpathwaysnetworklibsbmlcpp
4.71 score 19 scripts 1 dependentsbioc
ToxicoGx:Analysis of Large-Scale Toxico-Genomic Data
Contains a set of functions to perform large-scale analysis of toxicogenomic data, providing a standardized data structure to hold information relevant to annotation, visualization and statistical analysis of toxicogenomic data.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
geneexpressionpharmacogeneticspharmacogenomicssoftware
4.36 score 23 scripts
renkun-ken
rtype:A strong type system for R
A strong type system for R which supports symbol declaration and assignment with type checking and condition checking.
Maintained by Kun Ren. Last updated 11 years ago.
33 stars 4.22 score 5 scriptsbioc
XNAString:Efficient Manipulation of Modified Oligonucleotide Sequences
The XNAString package allows for description of base sequences and associated chemical modifications in a single object. XNAString is able to capture single stranded, as well as double stranded molecules. Chemical modifications are represented as independent strings associated with different features of the molecules (base sequence, sugar sequence, backbone sequence, modifications) and can be read or written to a HELM notation. It also enables secondary structure prediction using RNAfold from ViennaRNA. XNAString is designed to be efficient representation of nucleic-acid based therapeutics, therefore it stores information about target sequences and provides interface for matching and alignment functions from Biostrings and pwalign packages.
Maintained by Marianna Plucinska. Last updated 5 months ago.
sequencematchingalignmentsequencinggeneticscpp
4.18 score 4 scriptsr-forge
distrSim:Simulation Classes Based on Package 'distr'
S4-classes for setting up a coherent framework for simulation within the distr family of packages.
Maintained by Peter Ruckdeschel. Last updated 2 months ago.
4.16 score 7 scripts 3 dependents
pepijn-devries
ProTrackR:Manipulate and Play 'ProTracker' Modules
'ProTracker' is a popular music tracker to sequence music on a Commodore Amiga machine. This package offers the opportunity to import, export, manipulate and play 'ProTracker' module files. Even though the file format could be considered archaic, it still remains popular to this date. This package intends to contribute to this popularity and therewith keeping the legacy of 'ProTracker' and the Commodore Amiga alive.
Maintained by Pepijn de Vries. Last updated 3 months ago.
4 stars 4.12 score 66 scripts
simon-lenau
prolific.api:A User-Friendly Interface for Accessing the Prolific API
A user-friendly interface for creating and managing empirical crowd-sourcing studies via API access to <https://www.prolific.co>.
Maintained by Simon Lenau. Last updated 2 years ago.
crowd-sourcingcrowdsourcing-experimentscrowdsourcing-platformsempirical-researchparticipantssampling
3.70 score 8 scriptsbioc
R453Plus1Toolbox:A package for importing and analyzing data from Roche's Genome Sequencer System
The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche's 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.
Maintained by Hans-Ulrich Klein. Last updated 5 months ago.
sequencinginfrastructuredataimportdatarepresentationvisualizationqualitycontrolreportwriting
3.48 score 10 scriptsbioc
flowBin:Combining multitube flow cytometry data by binning
Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.
Maintained by Kieran ONeill. Last updated 5 months ago.
immunooncologycellbasedassaysflowcytometry
3.30 score 2 scripts
austinrwarner
tabulog:Parsing Semi-Structured Log Files into Tabular Format
Convert semi-structured log files (such as 'Apache' access.log files) into a tabular format (data.frame) using a standard template system.
Maintained by Austin Nar. Last updated 6 years ago.
2.70 score 5 scripts