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r-immunarch
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public |
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
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2025-09-25 |
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essspectroscopy
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public |
Spectroscopy data reduction for the European Spallation Source
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2025-09-25 |
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clarabel
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public |
Python interface for Clarabel: Interior Point Conic Optimization Solver
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2025-09-25 |
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r-ips
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public |
Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
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2025-09-25 |
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r-taxize
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public |
Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.
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2025-09-25 |
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r-phytools
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public |
A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
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2025-09-25 |
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hugo
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public |
The extended version of the Hugo static site generator – the world's fastest framework for building websites.
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2025-09-25 |
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act-atmos
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public |
Python library for working with atmospheric time-series by n-dimension datasets
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2025-09-25 |
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at-spi2-core
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public |
D-Bus-based implementation of AT-SPI accessibility framework
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2025-09-25 |
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arelle-release
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public |
Arelle is an end-to-end open source XBRL platform, which provides the XBRL community with an easy to use set of tools. It supports XBRL and its extension features in an extensible manner. It does this in a compact yet robust framework that can be used as a desktop application and can be integrated with other applications and languages utilizing its web service.
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2025-09-25 |
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sci-fab
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public |
Build system for scientific software
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2025-09-25 |
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eeglabio
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public |
I/O support for EEGLAB files in Python
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2025-09-25 |
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twilio
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public |
Twilio API client and TwiML generator
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2025-09-25 |
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r-ggwordcloud
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public |
Provides a word cloud text geom for 'ggplot2'. Texts are placed so that they do not overlap as in 'ggrepel'. The algorithm used is a variation around the one of 'wordcloud2.js'.
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2025-09-25 |
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tree-sitter-embedded-template
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public |
A tree-sitter parser for templating languages like ERB and EJS.
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2025-09-25 |
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skrub
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public |
Machine learning for dataframes
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2025-09-25 |
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r-paletteer
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public |
The choices of color palettes in R can be quite overwhelming with palettes spread over many packages with many different API's. This packages aims to collect all color palettes across the R ecosystem under the same package with a streamlined API.
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2025-09-25 |
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heudiconv
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public |
Heuristic DICOM Converter
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2025-09-25 |
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terraform-provider-grafana
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public |
The Terraform Grafana provider
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2025-09-25 |
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openfast
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public |
OpenFAST whole turbine simulation tool
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2025-09-25 |
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r-ggfittext
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public |
Provides 'ggplot2' geoms to fit text into a box by growing, shrinking or wrapping the text.
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2025-09-25 |
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r-ggtext
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public |
A 'ggplot2' extension that enables the rendering of complex formatted plot labels (titles, subtitles, facet labels, axis labels, etc.). Text boxes with automatic word wrap are also supported.
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2025-09-25 |
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lightly-train
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public |
Train models with self-supervised learning in a single command
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2025-09-25 |
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pyiron_potentialfit
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public |
Fitting machine learning interatomic potentials with pyiron.
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2025-09-25 |
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r-onewaytests
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public |
Performs one-way tests in independent groups designs including homoscedastic and heteroscedastic tests. These are one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
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2025-09-25 |
