qqman - Q-Q and Manhattan Plots for GWAS Data

Create Q-Q and manhattan plots for GWAS data from PLINK results.

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genomicsgwas

12.69 score 173 stars 20 dependents 3.2k scripts 6.0k downloads

rplanes - Plausibility Analysis of Epidemiological Signals

Provides functionality to prepare data and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausibility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score.

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5.78 score 10 stars 7 scripts 207 downloads

pracpac - Practical 'R' Packaging in 'Docker'

Streamline the creation of 'Docker' images with 'R' packages and dependencies embedded. The 'pracpac' package provides a 'usethis'-like interface to creating Dockerfiles with dependencies managed by 'renv'. The 'pracpac' functionality is described in Nagraj and Turner (2023) <doi:10.48550/arXiv.2303.07876>.

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5.60 score 40 stars 6 scripts 723 downloads

Tmisc - Turner Miscellaneous

Miscellaneous utility functions for data manipulation, data tidying, and working with gene expression data and biological sequence data.

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5.42 score 2 stars 1 dependents 220 scripts 383 downloads

skater - Utilities for SNP-Based Kinship Analysis

Utilities for single nucleotide polymorphism (SNP) based kinship analysis testing and evaluation. The 'skater' package contains functions for importing, parsing, and analyzing pedigree data, performing relationship degree inference, benchmarking relationship degree classification, and summarizing identity by descent (IBD) segment data. Package functions and methods are described in Turner et al. (2021) "skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation" <doi:10.1101/2021.07.21.453083>.

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5.40 score 10 stars 7 scripts 627 downloads

kgp - 1000 Genomes Project Metadata

Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) <doi:10.48550/arXiv.2210.00539> for more details.

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1000genomesbioinformaticsgeneticsgenomicsmetadatapopulation-geneticssequencing

4.02 score 21 stars 7 scripts 214 downloads

rpkgdemo - A demo package for building R packages

A package to demonstrate building an R package to accompany a workshop on building R packages in Positron. See the getting started vignette for details.

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3.95 score 6 stars 4 scripts

fiphde - Forecasting Influenza in Support of Public Health Decision Making

Miscellaneous functions for retrieving data, creating and evaluating time series forecasting models for influenza-like illness (ILI) and influenza hospitalizations in the United States.

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3.90 score 4 stars 10 scripts

biorecap - Retrieve and summarize bioRxiv and medRxiv preprints with a local LLM using ollama

Retrieve and summarize bioRxiv and medRxiv preprints with a local LLM using ollama.

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3.57 score 74 stars 5 scripts

hcop - What the Package Does (Title Case)

Human ortholog data from HGNC Comparison of Orthology Predictions (HCOP).

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2.88 score 15 stars 2 scripts

Tverse - Meta package that installs my most commonly used packages

Meta package that installs my most commonly used packages.

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quarto

2.70 score 10 stars

tfboot - Bootstrapping and statistical analysis for TFBS-disrupting SNPs

Bootstrap motifbreakR results for statistical analysis on TFBS-disrupting SNPs in upstream regions of a set of genes of interest.

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bioconductorbioinformatics

2.40 score 5 stars 3 scripts

rpdd - R package Docker Demo

Demonstrates using an R package inside a Docker image.

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2.00 score 2 stars 2 scripts

string2dna - Encode/Decode Strings as Nucleotide Sequences

Encode strings as nucleotide sequences and decode nucleotide sequences into strings.

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1.70 score 1 stars

focustools - Forecasting COVID-19 in the United States (FOCUS) tools

Miscellaneous functions for retrieving data, creating and evaluating time series forecasting models for COVID-19 cases and deaths in the United States. Built for participation in the COVID-19 Forecast Hub.

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1.70 score 4 scripts