bgruening
by bgruening
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| ambertools | 19 | AmberTools is a set of programs for biomolecular simulation and analysis | Mar 25, 2025 | GPL |
| antismash | 6.1.1 | antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell | Mar 25, 2025 | AGPL-3.0 |
| bioconductor-bgeedb | 2.36.0 | Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology | Mar 13, 2026 | GPL-3 + file LICENSE |
| bioconductor-biocgenerics | 0.17.3 | S4 generic functions needed by many Bioconductor packages. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-biostrings | 2.39.12 | Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-cardinal | 1.3.1 | Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-deseq2 | 1.11.38 | 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. | Mar 25, 2025 | LGPL (>= 3) |
| bioconductor-genomicfeatures | 1.23.27 | A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-genomicranges | 1.23.24 | The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages respectively. Both packages build on top of the GenomicRanges infrastructure. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-iranges | 2.5.40 | The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-omnipathr | 3.18.4 | OmniPath web service client and more | Feb 9, 2026 | MIT + file LICENSE |
| bioconductor-s4vectors | 0.9.44 | The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages). | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-summarizedexperiment | 1.1.22 | The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples. | Mar 25, 2025 | Artistic-2.0 |
| bioconductor-tximport | 0.99.8 | Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts. | Mar 25, 2025 | GPL (>=2) |
| bioconductor-xvector | 0.11.7 | Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk). | Mar 25, 2025 | Artistic-2.0 |
| cellprofiler | 3.1.9 | CellProfiler is free, open-source software for quantitative analysis of biological images | Mar 25, 2025 | 3-clause BSD |
| csem | 2.1.0 | The Community Earth System Model (CESM) is a coupled climate model for simulating Earth’s climate system | Mar 25, 2025 | BSD 3-Clause |
| dimspy | 1.2.0 | Python package for data processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data | Mar 25, 2025 | GPLv3 |
| eden | 1.0 | PyYAML-based module to produce pretty and readable YAML-serialized data | Mar 25, 2025 | WTFPL |
| funannotate | 1.8.17 | funannotate: eukaryotic genome annotation pipeline | Mar 25, 2025 | BSD-2-Clause |
| libopenms | 2.6.0dev | OpenMS is an open-source software C++ library for LC-MS data management and analyses | Mar 25, 2025 | BSD |
| lofreq | 2.1.4 | A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data | Mar 25, 2025 | MIT |
| moff | 0.1 | A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file | Mar 25, 2025 | GPL |
| nucleosome_prediction | 3.0 | — | Mar 25, 2025 | — |
| openms | 2.6.0dev | OpenMS is an open-source software C++ library for LC-MS data management and analyses | Mar 25, 2025 | BSD |