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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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public |
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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public |
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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public |
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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public |
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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public |
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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public |
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 |
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r-rgcca
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public |
Multiblock data analysis concerns the analysis of several sets of variables (blocks) observed on the same group of individuals. The main aims of the RGCCA package are: (i) to study the relationships between blocks and (ii) to identify subsets of variables of each block which are active in their relationships with the other blocks.
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2025-09-23 |
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r-gpseq
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public |
Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.
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2025-09-23 |
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r-funrar
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public |
Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
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2025-09-23 |
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r-debugr
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public |
Tool to print out the value of R objects/expressions while running an R script. Outputs can be made dependent on user-defined conditions/criteria. Debug messages only appear when a global option for debugging is set. This way, 'debugr' code can even remain in the debugged code for later use without any negative effects during normal runtime.
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2025-09-23 |
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r-nlcoptim
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public |
Optimization for nonlinear objective and constraint functions. Linear or nonlinear equality and inequality constraints are allowed. It accepts the input parameters as a constrained matrix.
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2025-09-23 |
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r-sciplot
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public |
A collection of functions that creates graphs with error bars for data collected from one-way or higher factorial designs.
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2025-09-23 |
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r-fdasrvf
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public |
Performs alignment, PCA, and modeling of multidimensional and unidimensional functions using the square-root velocity framework (Srivastava et al., 2011 <arXiv:1103.3817> and Tucker et al., 2014 <DOI:10.1016/j.csda.2012.12.001>). This framework allows for elastic analysis of functional data through phase and amplitude separation.
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2025-09-23 |
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r-hrbrthemes
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public |
A compilation of extra 'ggplot2' themes, scales and utilities, including a spell check function for plot label fields and an overall emphasis on typography. A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/> is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type> and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts are also included to support their respective typography-oriented themes.
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2025-09-23 |
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r-flextable
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public |
Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.
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2025-09-23 |
