genomation - Summary, annotation and visualization of genomic data

A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

Last updated 24 days ago

annotationsequencingvisualizationcpgisland

10.94 score 74 stars 5 packages 560 scripts 1.0k downloads

netSmooth - Network smoothing for scRNAseq

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

Last updated 24 days ago

networkgraphandnetworksinglecellrnaseqgeneexpressionsequencingtranscriptomicsnormalizationpreprocessingclusteringdimensionreductionbioinformaticsgenomicssingle-cell

7.41 score 27 stars 4 scripts 212 downloads

mergen - AI-Driven Code Generation, Explanation and Execution for Data Analysis

Employing artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. The self-correction feature ensures the generated code is optimized for performance and accuracy. 'mergen' features a user-friendly chat interface, enabling users to interact with the AI agent and extract valuable insights from their data effortlessly.

Last updated 2 months ago

6.60 score 12 stars 1 packages 3 scripts 251 downloads

deconvR - Simulation and Deconvolution of Omic Profiles

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

Last updated 24 days ago

dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics

5.75 score 10 stars 14 scripts 264 downloads

guix.install - Install R Packages with GNU Guix

This 'R' package provides a single procedure guix.install(), which allows users to install 'R' packages via 'Guix' right from within their running 'R' session. If the requested 'R' package does not exist in 'Guix' at this time, the package and all its missing dependencies will be imported recursively and the generated package definitions will be written to ~/.Rguix/packages.scm. This record of imported packages can be used later to reproduce the environment, and to add the packages in question to a proper 'Guix' channel (or 'Guix' itself). guix.install() not only supports installing packages from CRAN, but also from Bioconductor or even arbitrary 'git' or 'mercurial' repositories, replacing the need for installation via 'devtools'.

Last updated 2 years ago

2.48 score 3 stars 105 downloads