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r-oceanview
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public |
Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
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2025-09-23 |
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r-rapport
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public |
Facilitating the creation of reproducible statistical report templates. Once created, rapport templates can be exported to various external formats (HTML, LaTeX, PDF, ODT etc.) with pandoc as the converter backend.
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2025-09-23 |
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r-aggregation
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public |
Contains functionality for performing the following methods of p-value aggregation: Fisher's method [Fisher, RA (1932, ISBN: 9780028447308)], the Lancaster method (weighted Fisher's method) [Lancaster, HO (1961, <doi:10.1111/j.1467-842X.1961.tb00058.x>)], and Sidak correction [Sidak, Z (1967, <doi:10.1080/01621459.1967.10482935>)]. Please cite Yi et al., the manuscript corresponding to this package [Yi, L et al., (2017), <doi:10.1101/190199>].
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2025-09-23 |
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r-discriminer
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public |
Functions for Discriminant Analysis and Classification purposes covering various methods such as descriptive, geometric, linear, quadratic, PLS, as well as qualitative discriminant analyses
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2025-09-23 |
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r-infuser
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public |
This light-weight templating package provides flexible and user-friendly value substitution in string templates or template files (e.g. SQL files) at runtime.
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2025-09-23 |
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r-gghighlight
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public |
Make it easier to explore data with highlights.
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2025-09-23 |
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jax
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public |
Differentiate, compile, and transform Numpy code
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2025-09-23 |
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r-incadata
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public |
Handle data in formats used by cancer centers in Sweden, both from 'INCA' (<https://rcc.incanet.se>) and by the older register platform 'Rockan'. All variables are coerced to suitable classes based on their format. Dates (from various formats such as with missing month or day, with or without century prefix or with just a week number) are all recognized as dates and coerced to the ISO 8601 standard (Y-m-d). Boolean variables (internally stored either as 0/1 or "True"/"False"/blanks when exported) are coerced to logical. Variable names ending in '_Beskrivning' and '_Varde' will be character, and 'PERSNR' will be coerced (if possible) to a valid personal identification number 'pin' (by the 'sweidnumbr' package). The package also allow the user to interactively choose if a variable should be coerced into a potential format even though not all of its values might conform to the recognized pattern. It also contain a caching mechanism in order to temporarily store data sets with its newly decided formats in order to not rerun the identification process each time. The package also include a mechanism to aid the documentation process connected to projects build on data from 'INCA'. From version 0.7, some general help functions are also included, as previously found in the 'rccmisc' package.
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2025-09-23 |
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r-chromomap
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public |
Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the large size of the chromosomes, it is impractical to visualize each element on the same plot. However, the plot provides a magnified view for each of chromosome locus to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. The plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R 'Shiny' applications.
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2025-09-23 |
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supervisor-pydantic
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public |
Pydantic models for supervisor
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2025-09-23 |
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r-drtmle
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public |
Targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality (Benkeser et al (2017), <doi:10.1093/biomet/asx053>; MJ van der Laan (2014), <doi:10.1515/ijb-2012-0038>).
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2025-09-23 |
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r-soniclength
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Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence `sonicLength'). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.
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2025-09-23 |
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r-paws
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public |
Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.
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2025-09-23 |
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r-daff
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Diff, patch and merge for data frames. Document changes in data sets and use them to apply patches. Changes to data can be made visible by using render_diff. The V8 package is used to wrap the 'daff.js' JavaScript library which is included in the package.
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2025-09-23 |
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ydata-profiling
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public |
Generate profile report for pandas DataFrame
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2025-09-23 |
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r-thief
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public |
Methods and tools for generating forecasts at different temporal frequencies using a hierarchical time series approach.
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2025-09-23 |
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gh
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public |
Github CLI.
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2025-09-23 |
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cypress
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public |
Fast, easy and reliable testing for anything that runs in a browser.
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2025-09-23 |
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r-aleplot
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public |
Visualizes the main effects of individual predictor variables and their second-order interaction effects in black-box supervised learning models. The package creates either Accumulated Local Effects (ALE) plots and/or Partial Dependence (PD) plots, given a fitted supervised learning model.
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2025-09-23 |
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r-bedr
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public |
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
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2025-09-23 |
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r-librarian
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public |
Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor' packages in a single function call. By accepting bare unquoted names for packages, it's easy to add or remove packages from the list.
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2025-09-23 |
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r-projmgr
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Provides programmatic access to 'GitHub' API with a focus on project management. Key functionality includes setting up issues and milestones from R objects or 'YAML' configurations, querying outstanding or completed tasks, and generating progress updates in tables, charts, and RMarkdown reports. Useful for those using 'GitHub' in personal, professional, or academic settings with an emphasis on streamlining the workflow of data analysis projects.
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2025-09-23 |
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r-precommit
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Useful git hooks for R building on top of the multi-language framework 'pre-commit' for hook management. This package provides git hooks for common tasks like formatting files with 'styler' or spell checking as well as wrapper functions to access the 'pre-commit' executable.
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2025-09-23 |
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r-hiver
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Creates and plots 2D and 3D hive plots. Hive plots are a unique method of displaying networks of many types in which node properties are mapped to axes using meaningful properties rather than being arbitrarily positioned. The hive plot concept was invented by Martin Krzywinski at the Genome Science Center (www.hiveplot.net/). Keywords: networks, food webs, linnet, systems biology, bioinformatics.
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2025-09-23 |
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r-carrier
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Sending functions to remote processes can be wasteful of resources because they carry their environments with them. With the carrier package, it is easy to create functions that are isolated from their environment. These isolated functions, also called crates, print at the console with their total size and can be easily tested locally before being sent to a remote.
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2025-09-23 |
