ggseqlogo - A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos
The extensive range of functions provided by this package makes it possible to draw highly versatile sequence logos. Features include, but not limited to, modifying colour schemes and fonts used to draw the logo, generating multiple logo plots, and aiding the visualisation with annotations. Sequence logos can easily be combined with other plots 'ggplot2' plots.
Last updated 7 months ago
200 stars 6.73 score 28 dependencies 12 dependentsArchR - Analyzing single-cell regulatory chromatin in R.
This package is designed to streamline scATAC analyses in R.
Last updated 7 months ago
371 stars 6.63 score 177 dependenciesmonocle3 - Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq
Monocle 3 performs clustering, differential expression and trajectory analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle 3 also performs differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. It is designed to work with RNA-Seq data, but could be used with other types as well.
Last updated 5 months ago
single-cell-rna-seq
324 stars 6.40 score 184 dependencies 2 dependentsRcppRoll - Efficient Rolling / Windowed Operations
Provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.
Last updated 2 months ago
83 stars 6.21 score 1 dependencies 60 dependents![](https://github.com/leeper/margins/raw/HEAD/man/figures/logo.png)
margins - Marginal Effects for Model Objects
An R port of Stata's 'margins' command, which can be used to calculate marginal (or partial) effects from model objects.
Last updated 4 years ago
glmlinear-modelsmarginal-effectspartial-effectsregressionstata-command
260 stars 6.00 score 3 dependencies 1 dependentsBPCells - Single Cell Counts Matrices to PCA
> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.
Last updated 3 months ago
148 stars 5.02 score 42 dependenciesDDRTree - Learning Principal Graphs with DDRTree
Project data into a reduced dimensional space and construct a principal graph from the reduced dimension.
Last updated 6 years ago
4 stars 4.63 score 6 dependencies 3 dependentsSeuratData - Install and Manage Seurat Datasets
Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.
Last updated 10 months ago
datasetssingle-cellsingle-cell-genomics
119 stars 4.44 score 23 dependenciesAzimuth - A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Azimuth uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery).
Last updated 10 months ago
shiny-appsingle-cell-genomicssingle-cell-rna-seq
103 stars 4.25 score 241 dependenciesloupeR - Converts Seurat objects to 10x Genomics Loupe files
Converts Seurat objects to 10x Genomics Loupe files. This is a second line to make the package checker not complain.
Last updated 2 months ago
10xgenomicssingle-cell-genomics
86 stars 4.03 score 149 dependenciesdotwhisker - Dot-and-Whisker Plots of Regression Results
Quick and easy dot-and-whisker plots of regression results.
Last updated 19 days ago
graphicsplotregression-models
57 stars 3.77 score 44 dependenciesmdthemes - Markdown Themes for 'ggplot2'
A collection of 'ggplot2' themes that render text as markdown/HTML. This enables the creation of complex formatted plot labels, e.g. titles with individual words highlighted in different colors.
Last updated 3 years ago
79 stars 3.68 score 59 dependenciespenalized - L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model
Fitting possibly high dimensional penalized regression models. The penalty structure can be any combination of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity constraint on the regression coefficients. The supported regression models are linear, logistic and Poisson regression and the Cox Proportional Hazards model. Cross-validation routines allow optimization of the tuning parameters.
Last updated 2 years ago
3 stars 3.26 score 5 dependencies 15 dependentsrdoc - Colourised R Documentation
Extends tools::Rd2txt() by adding customisable text and colour formatting to R documentation contents. If used from a terminal, output will be displayed via file.show() otherwise contents will be printed in sections. Also provides stand-in replacements for ?() and help().
Last updated 5 years ago
clicolorizationcrayondocumentationpretty-print
49 stars 2.89 score 4 dependencies![](https://github.com/jeffsocal/tidyproteomics/raw/HEAD/man/figures/logo.png)
tidyproteomics - An S3 data object and framework for common quantitative proteomic analyses
Creates a simple, universal S3 data structure for the post analysis of mass spectrometry based quantitative proteomic data. In addition, this package collects, adapts and organizes several useful algorithms and methods used in typical post analysis workflows.
Last updated 1 months ago
30 stars 2.70 score 103 dependenciesspeedglm - Fitting Linear and Generalized Linear Models to Large Data Sets
Fitting linear models and generalized linear models to large data sets by updating algorithms.
Last updated 3 years ago
5 stars 2.57 score 3 dependencies 11 dependentsblaseRtools - R Tools for Blaser Lab Data Analysis
This is a repository of R tools for Single Cell RNA seq and other lab data analysis functions.
Last updated 3 months ago
1.58 score 401 dependenciesblaseRtemplates - Generates a structured R project with custom templates.
This package generates an R project with customized templates. It also packages bash scripts for blaserlab collaborative git workflow.
Last updated 1 months ago
1.16 score 111 dependencies 1 dependentsmhurdle - Multiple Hurdle Tobit Models
Estimation of models with dependent variable left-censored at zero. Null values may be caused by a selection process Cragg (1971) <doi:10.2307/1909582>, insufficient resources Tobin (1958) <doi:10.2307/1907382>, or infrequency of purchase Deaton and Irish (1984) <doi:10.1016/0047-2727(84)90067-7>.
Last updated 3 months ago
0.89 score 25 dependenciesDAseq - Detecting regions of differential abundance between scRNA-seq datasets
DA-seq is a multiscale approach for detecting DA subpopulations. In contrast to clustering based approaches, our method can detect DA subpopulations that do not form well separated clusters. For each cell, we compute a multiscale differential abundance score measure. These scores are based on the k nearest neighbors in the transcriptome space for various values of k.
Last updated 3 years ago
39 stars 2.57 score 172 dependenciesgenbankr - Parsing GenBank files into semantically useful objects
Reads Genbank files.
Last updated 11 months ago
14 stars 1.90 score 70 dependenciesRforMassSpectrometry - R for MassSpectrometry meta-package
The RforMassSpectrometry meta-package loads and manages the core packages of the R for Mass Spectrometry initiative, that provide efficient, thoroughly documented, tested and flexible R software for the analysis and interpretation of high throughput mass spectrometry assays.
Last updated 9 months ago
15 stars 1.64 score 112 dependenciesGOsummaries - Word cloud summaries of GO enrichment analysis
A package to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarising the underlying data.
Last updated 6 years ago
11 stars 1.38 score 38 dependenciesblaseRdata - Supporting Data for the blaseRtools Package
What the package does (one paragraph).
Last updated 5 months ago
0.71 score 197 dependencies 1 dependentsChrAccR - Analyzing chromatin accessibility data in R
Tools for analyzing chromatin accessibility data in R. Bulk and single-cell ATAC-seq data are supported.
Last updated 1 years ago
16 stars 1.51 score 70 dependenciesTxDb.Drerio.UCSC.danRer11.ensGene - Annotation package for TxDb object(s)
Exposes an annotation databases generated from UCSC by exposing these as TxDb objects
Last updated 1 years ago
0.36 score 68 dependencies 1 dependentsmuRtools - Mueller's R tools
Fabian's custom plotting functions and utilities
Last updated 1 years ago
1 stars 0.23 score 46 dependenciesdatascience.curriculum - Data Science 2023
What the package does (one paragraph).
Last updated 1 years ago
1 stars 0.09 score 134 dependenciesmuReportR - muReportR
Generate HTML reports from R. Based on code from the RnBeads package.
Last updated 5 years ago
0.00 score 28 dependenciesmuLogR - muLogR
Logging and code structuring for R. Based on code from the RnBeads package.
Last updated 5 years ago
0.00 score 0 dependencies