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74 search results found

Tidy Text Mining ⭐ 1,239

Manuscript of the book "Tidy Text Mining with R" by Julia Silge and David Robinson

📜 🎉 Automated reporting of objects in R

papaja (Preparing APA Journal Articles) is an R package that provides document formats to produce complete APA manuscripts from RMarkdown-files (PDF and Word documents) and helper functions that facilitate reporting statistics, tables, and plots.

Harmony ⭐ 460

Fast, sensitive and accurate integration of single-cell data with Harmony

Bibliometrix ⭐ 440

An R-tool for comprehensive science mapping analysis. A package for quantitative research in scientometrics and bibliometrics.

Dynbenchmark ⭐ 167

Comparison of methods for trajectory inference on single-cell data 🥇

Statcheck ⭐ 162

A spellchecker for statistics

Rmdtemplates ⭐ 119

Rmarkdown templates for reproducible science

Sciclone ⭐ 112

An R package for inferring the subclonal architecture of tumors

Psycho.r ⭐ 110

An R package for experimental psychologists

Stevetemplates ⭐ 100

My collection of R Markdown templates, as an R package.

Template ⭐ 85

📦 A template for my research projects, based on the R package structure

Rforproteomics ⭐ 69

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Variancepartition ⭐ 48

Quantify and interpret divers of variation in multilevel gene expression experiments

Living Documents ⭐ 47

How to use Jupyter notebooks and R markdown to create living documents and reproducible reports.

Manuscriptpackage ⭐ 46

Template for writing manuscripts as an R package

Anovapower ⭐ 28

Simulation-Based Power Analysis for ANOVA Designs

Laketrophicmodelling ⭐ 26

ORD LakeTrophicModelling

Make Example ⭐ 25

An example of using make for a data analysis project

Scrna_cell_deconv_benchmark ⭐ 24

Evaluation of Cell Type Annotation R Packages on Single Cell RNA-seq Data

Windows version of StatTag

Gnomad Sv Pipeline ⭐ 22

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)

Tumor Immunogenicity Score ⭐ 21

TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020

How much of the world is woody?

Rnamagnet ⭐ 18

Pleurosoriopsis ⭐ 17

Growth Dynamics of the Independent Gametophytes of Pleurorosiopsis makinoi (Polypodiaceae)

Metagenomics calibration R package

Psupertime ⭐ 13

psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels

Mito Genotyping ⭐ 13

Repo for scripts for Ludwig et al mtDNA genotyping

Covidcompare ⭐ 13

Global COVID-19 Forecast Comparison

LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution analyses for single-cell sequencing data, including longitudinal experiments. The tool also allows to annotate and retrieve the relevant variants based on user-defined criteria.

Minimaltemplate ⭐ 11

A R package to create a minimal template for scientific manuscripts in .docx

Frequencyfilter ⭐ 11

Allele frequency filtering for Mendelian variant discovery

Traveller_screening ⭐ 10

Code for analyses in 2020 nCoV preprint, based on analyses from Gostic et al., eLife, 2015.

Cpcrw_incubation ⭐ 10

PNNL TES incubation of CPCRW soil cores #openexperiment

Sparsesignatures ⭐ 10

Extracting mutational signatures via LASSO. The manuscript of the method is published on PLOS Computational Biology and available at: https://journals.plos.org/ploscompbiol/article?id=

Tapseq_manuscript ⭐ 10

Analysis code for the TAP-seq manuscript.

Repressivecapacity ⭐ 9

Reanalysis of the repressive capacity of promoter DNA methylation

Deep Treatment Learning (R)

Celligner_ms ⭐ 8

Code related to the Celligner manuscript

Prnp_penetrance ⭐ 7

Analysis of the penetrance of missense variants and tolerability of loss-of-function variants in PRNP

R package for MGC code

Deep Compositional Spatial Models

A user-friendly spatial tool with a web-based interface that allows users to import SDM layers and create and explore ensemble predictions to inform management and explore spatial uncertainties

Gtex Admixture La ⭐ 6

Code accompanying "Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx"

High_dimensional_regression_comparison ⭐ 6

Empirical comparison of penalized linear regression in high-dimensional settings

Manuscript Dnns For Classification Of Lcms Peaks ⭐ 6

Code associated with the manuscript: Deep Neural Networks for Classification of LC-MS Spectral Peaks

Ballgown_code ⭐ 6

analysis code used in Ballgown paper

Te Driven Ctcf Loop Evol ⭐ 6

Hausekeep ⭐ 6

R package with functions to improve research workflow https://hauselin.github.io/hausekeep/

Tdmresults ⭐ 6

Scripts and data for re-creating TDM results.

Composite Mutations ⭐ 6

Companion code to the paper "Phase and context shapes the function of composite oncogenic mutations"

Viral Evolution ReconStructiOn (VERSO). The manuscript of the method is available at: https://www.cell.com/patterns/fulltext/S2666-3899(

Scft Paper ⭐ 6

Z Hu et al. The repertoire of serous ovarian cancer non-genetic heterogeneity revealed by single-cell sequencing of normal fallopian tube epithelial cells. Cancer Cell (2020). Volume 37, Issue 2, P226-242

Genotype_networks ⭐ 6

code, data, and manuscript for the PNAS paper: "Genetic specificity of a plant-insect food web: implications for linking genetic variation to network complexity".

Door.data ⭐ 6

R package containing the data for the Database of Odor Responses

Pregnancy_cfrna ⭐ 6

Repository to reproduce analyses from manuscript titled "Noninvasive blood tests for fetal development predict gestational age and preterm delivery"

Crosslong ⭐ 5

Nature is a language---can't you read?

Markdownms ⭐ 5

A skeleton academic manuscript in markdown

Hmp Oral Microbiota ⭐ 5

Some data files and scripts for our oligotyping analysis of human oral microbiota.

R-Codes for RSE manuscript "Importance of sample size, data type and prediction method for remote sensing-based estimations of aboveground forest biomass"

Extreme Events Lda ⭐ 5

Quantifying dynamics of rodent community at Portal, using LDA

MIMICS Code Repository

Treeuncertainty ⭐ 5

Incorporating uncertainty in tree space

Suite of Tools for ET-seq Informatic Workflow

Forestviews ⭐ 5

visualise paths through random forests:

Oncoscore ⭐ 5

OncoScore is a tool to measure the association of genes to cancer based on citation frequency in biomedical literature. The manuscript of the method is published on Scientific Reports and available at http://www.nature.com/articles/srep46290. The tool can also be used as a Web interface at https://www.galseq.com/next-generation-sequencing/

Predator_phylogenetic_diversity ⭐ 5

predator phylogenetic diversity / ecosystem function

Interactive ⭐ 5

interActive Application Source Code

Biome_specific_predictability ⭐ 5

Calculating temperature and precipitation predictability at the global scale

Expectedforce ⭐ 5

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