huber-group-embl.r-universe.dev

[huber-group-embl] Rarr 2.1.18

hugo.gruson@embl.de (Hugo Gruson) — Wed, 10 Jun 2026 13:25:16 GMT

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.

[bioc] Rarr 2.1.18

hugo.gruson@embl.de (Hugo Gruson) — Wed, 10 Jun 2026 13:25:16 GMT

[huber-group-embl] rhdf5 2.57.1

hugo.gruson@embl.de (Hugo Gruson) — Wed, 27 May 2026 06:59:06 GMT

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

[bioc] rhdf5 2.57.1

hugo.gruson@embl.de (Hugo Gruson) — Tue, 26 May 2026 07:18:55 GMT

[huber-group-embl] lemur 1.11.1

artjom31415@googlemail.com (Constantin Ahlmann-Eltze) — Tue, 19 May 2026 09:42:28 GMT

Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.

[bioc] arrayQualityMetrics 3.69.1

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 17:28:11 GMT

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

[huber-group-embl] arrayQualityMetrics 3.69.1

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 17:28:11 GMT

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

[bioc] DepInfeR 1.17.0

jylu1118@gmail.com (Junyan Lu) — Tue, 28 Apr 2026 12:58:04 GMT

DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.

[bioc] rhdf5filters 1.25.0

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 12:52:04 GMT

Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.

[huber-group-embl] Rhdf5lib 2.1.0

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 12:45:53 GMT

Provides C and C++ hdf5 libraries.

[bioc] Rhdf5lib 2.1.0

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 12:45:53 GMT

Provides C and C++ hdf5 libraries.

[bioc] lpsymphony 1.41.0

vladislav.kim@embl.de (Vladislav Kim) — Tue, 28 Apr 2026 12:42:21 GMT

This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.

[huber-group-embl] HilbertVis 1.71.0

sanders@fs.tum.de (Simon Anders) — Tue, 28 Apr 2026 12:33:32 GMT

Functions to visualize long vectors of integer data by means of Hilbert curves

[huber-group-embl] splots 1.79.0

wolfgang.huber@embl.org (Wolfgang Huber) — Tue, 28 Apr 2026 12:31:55 GMT

This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.

[huber-group-embl] MSMB 1.31.0

wolfgang.huber@embl.org (Wolfgang Huber) — Tue, 28 Apr 2026 12:31:34 GMT

Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber.

[bioc] biomaRt 2.69.0

hugo.gruson@embl.de (Hugo Gruson) — Tue, 28 Apr 2026 12:30:57 GMT

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintained by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.

[bioc] vsn 3.81.0

wolfgang.huber@embl.org (Wolfgang Huber) — Tue, 28 Apr 2026 12:30:04 GMT

The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

[huber-group-embl] DEXSeq 1.57.2

hugo.gruson@embl.de (Hugo Gruson) — Sun, 12 Apr 2026 12:56:04 GMT

The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

[huber-group-embl] biomaRt 2.67.7

hugo.gruson@embl.de (Hugo Gruson) — Tue, 07 Apr 2026 10:21:05 GMT

[huber-group-embl] vsn 3.79.6

wolfgang.huber@embl.org (Wolfgang Huber) — Fri, 27 Mar 2026 13:22:05 GMT

[huber-group-embl] DESeq2 1.51.7

michaelisaiahlove@gmail.com (Michael Love) — Thu, 12 Mar 2026 17:58:58 GMT

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

[huber-group-embl] rhdf5filters 1.23.3

hugo.gruson@embl.de (Hugo Gruson) — Tue, 09 Dec 2025 15:31:48 GMT

[huber-group-embl] EBImage 4.47.1

andrzej.oles@gmail.com (Andrzej Oleś) — Mon, 14 Oct 2024 22:35:40 GMT

EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.

[huber-group-embl] IHW 1.29.0

nikos.ignatiadis01@gmail.com (Nikos Ignatiadis) — Tue, 25 Apr 2023 14:43:54 GMT

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.