|
r-ccremover
|
public |
Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) <doi
|
2025-04-22 |
|
r-log4r
|
public |
The log4r package is meant to provide a fast, lightweight, object-oriented approach to logging in R based on the widely-emulated 'log4j' system and etymology.
|
2025-04-22 |
|
r-tfmpvalue
|
public |
In putative Transcription Factor Binding Sites (TFBSs) identification from sequence/alignments, we are interested in the significance of certain match score. TFMPvalue provides the accurate calculation of P-value with score threshold for Position Weight Matrices, or the score with given P-value. It is an interface to code originally made available by Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15. Touzet and Varre (2007) <DOI:10.1186/1748-7188-2-15>.
|
2025-04-22 |
|
r-liblinear
|
public |
A wrapper around the LIBLINEAR C/C++ library for machine learning.
|
2025-04-22 |
|
r-readmzxmldata
|
public |
Functions for reading mass spectrometry data in mzXML format.
|
2025-04-22 |
|
r-glasso
|
public |
Estimation of a sparse inverse covariance matrix using a lasso (L1) penalty. Facilities are provided for estimates along a path of values for the regularization parameter.
|
2025-04-22 |
|
r-readbrukerflexdata
|
public |
Reads data files acquired by Bruker Daltonics' matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer of the *flex series.
|
2025-04-22 |
|
r-rda
|
public |
Shrunken Centroids Regularized Discriminant Analysis for the classification purpose in high dimensional data.
|
2025-04-22 |
|
r-protviz
|
public |
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
|
2025-04-22 |
|
r-matrixeqtl
|
public |
Matrix eQTL is designed for fast eQTL analysis on large datasets. Matrix eQTL can test for association between genotype and gene expression using linear regression with either additive or ANOVA genotype effects. The models can include covariates to account for factors as population stratification, gender, and clinical variables. It also supports models with heteroscedastic and/or correlated errors, false discovery rate estimation and separate treatment of local (cis) and distant (trans) eQTLs. For more details see Shabalin (2012) <doi:10.1093/bioinformatics/bts163>.
|
2025-04-22 |
|
r-seqinr
|
public |
Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 <doi:10.1093/nar/12.1Part1.121>.
|
2025-04-22 |
|
r-rphylip
|
public |
Rphylip provides an R interface for the PHYLIP package. All users of Rphylip will thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP.
|
2025-04-22 |
|
r-mrmre
|
public |
Computes mutual information matrices from continuous, categorical and survival variables, as well as feature selection with minimum redundancy, maximum relevance (mRMR) and a new ensemble mRMR technique.
|
2025-04-22 |
|
r-haplo.stats
|
public |
Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are
|
2025-04-22 |
|
r-gwidgets
|
public |
gWidgets provides a toolkit-independent API for building interactive GUIs. At least one of the 'gWidgetsXXX packages', such as gWidgetstcltk, needs to be installed. Some icons are on loan from the scigraphica project http
|
2025-04-22 |
|
r-dynamictreecut
|
public |
Contains methods for detection of clusters in hierarchical clustering dendrograms.
|
2025-04-22 |
|
r-desolve
|
public |
Functions that solve initial value problems of a system of first-order ordinary differential equations ('ODE'), of partial differential equations ('PDE'), of differential algebraic equations ('DAE'), and of delay differential equations. The functions provide an interface to the FORTRAN functions 'lsoda', 'lsodar', 'lsode', 'lsodes' of the 'ODEPACK' collection, to the FORTRAN functions 'dvode', 'zvode' and 'daspk' and a C-implementation of solvers of the 'Runge-Kutta' family with fixed or variable time steps. The package contains routines designed for solving 'ODEs' resulting from 1-D, 2-D and 3-D partial differential equations ('PDE') that have been converted to 'ODEs' by numerical differencing.
|
2025-04-22 |
|
r-rcppannoy
|
public |
'Annoy' is a small C++ library for Approximate Nearest Neighbors written for efficient memory usage as well an ability to load from / save to disk. This package provides an R interface by relying on the 'Rcpp' package, exposing the same interface as the original Python wrapper to 'Annoy'. See <https://github.com/spotify/annoy> for more on 'Annoy'. 'Annoy' is released under Version 2.0 of the Apache License. Also included is a small Windows port of 'mmap' which is released under the MIT license.
|
2025-04-22 |
|
r-purbayes
|
public |
PurBayes is an MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
|
2025-04-22 |
|
r-pcit
|
public |
Apply Partial Correlation coefficient with Information Theory (PCIT) to a correlation matrix. The PCIT algorithm identifies meaningful correlations to define edges in a weighted network. The algorithm can be applied to any correlation-based network including but not limited to gene co-expression networks. To reduce compute time by making use of multiple compute cores, simply run PCIT on a computer with has multiple cores and also has the Rmpi package installed. PCIT will then auto-detect the multicore environment and run in parallel mode without the need to rewrite your scripts. This makes scripts, using PCIT, portable across single core (or no Rmpi package installed) computers which will run in serial mode and multicore (with Rmpi package installed) computers which will run in parallel mode.
|
2025-04-22 |
|
r-icluster
|
public |
Integrative clustering of multiple genomic data types using a joint latent variable model.
|
2025-04-22 |
|
r-filehash
|
public |
Implements a simple key-value style database where character string keys are associated with data values that are stored on the disk. A simple interface is provided for inserting, retrieving, and deleting data from the database. Utilities are provided that allow 'filehash' databases to be treated much like environments and lists are already used in R. These utilities are provided to encourage interactive and exploratory analysis on large datasets. Three different file formats for representing the database are currently available and new formats can easily be incorporated by third parties for use in the 'filehash' framework.
|
2025-04-22 |
|
r-argumentcheck
|
public |
The typical process of checking arguments in functions is iterative. In this process, an error may be returned and the user may fix it only to receive another error on a different argument. 'ArgumentCheck' facilitates a more helpful way to perform argument checks allowing the programmer to run all of the checks and then return all of the errors and warnings in a single message.
|
2025-04-22 |
|
powerline-status
|
public |
Powerline is a statusline plugin for vim
|
2025-04-22 |
|
r-squash
|
public |
Functions for color-based visualization of multivariate data, i.e. colorgrams or heatmaps. Lower-level functions map numeric values to colors, display a matrix as an array of colors, and draw color keys. Higher-level plotting functions generate a bivariate histogram, a dendrogram aligned with a color-coded matrix, a triangular distance matrix, and more.
|
2025-04-22 |
