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r-allelicseries
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public |
Implementation of gene-level rare variant association tests targeting allelic series: genes where increasingly deleterious mutations have increasingly large phenotypic effects. The COding-variant Allelic Series Test (COAST) operates on the benign missense variants (BMVs), deleterious missense variants (DMVs), and protein truncating variants (PTVs) within a gene. COAST uses a set of adjustable weights that tailor the test towards rejecting the null hypothesis for genes where the average magnitude of effect increases monotonically from BMVs to DMVs to PTVs. See McCaw ZR, Somineni H, Bereket M, Klein C, Karaletsos T, Casale FP, Koller D, Soare TW. (2022) "An allelic series rare variant association test for candidate gene discovery" <doi:10.1101/2022.12.23.521658>.
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2025-09-23 |
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dotenvx
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public |
a better dotenv–from the creator of `dotenv`
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2025-09-23 |
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r-survauc
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public |
The package provides a variety of functions to estimate time-dependent true/false positive rates and AUC curves from a set of censored survival data.
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2025-09-23 |
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r-idpmisc
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public |
The IDPmisc package contains different high-level graphics functions for displaying
large datasets, displaying circular data in a very flexible way, finding local maxima,
brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with
differently colored margin and plot region. In addition, the package contains auxiliary
functions for data manipulation like omitting observations with irregular values
or selecting data by logical vectors, which include NAs. Other functions are especially
useful in spectroscopy and analyses of environmental data: robust baseline fitting,
finding peaks in spectra.
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2025-09-23 |
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r-uiucthemes
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public |
A set of custom 'R' 'Markdown' templates for documents and presentations with the University of Illinois at Urbana-Champaign (UIUC) color scheme and identity standards.
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2025-09-23 |
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r-pathmodelfit
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public |
Functions for computing fit indices for evaluating the path component of latent variable structural equation models. Available fit indices include RMSEA-P and NSCI-P originally presented and evaluated by Williams and O'Boyle (2011) <doi:10.1177/1094428110391472> and demonstrated by O'Boyle and Williams (2011) <doi:10.1037/a0020539> and Williams, O'Boyle, & Yu (2020) <doi:10.1177/1094428117736137>. Also included are fit indices described by Hancock and Mueller (2011) <doi:10.1177/0013164410384856>.
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2025-09-23 |
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r-gmwt
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public |
Generalized Mann-Whitney type tests based on probabilistic indices and new diagnostic plots, for the underlying manuscript see Fischer, Oja (2015) <doi:10.18637/jss.v065.i09>.
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2025-09-23 |
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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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mypy_boto3_ec2
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public |
Type annotations for boto3.EC2 1.40.37 service, generated by mypy-boto3-builder
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2025-09-23 |
