ArchR - Analyzing single-cell regulatory chromatin in R.

This package is designed to streamline scATAC analyses in R.

Last updated 2 hours ago

cpp

7.94 score 398 stars 2.4k scripts

RcppRoll - 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 8 months ago

cpp

10.89 score 82 stars 63 dependents 1.8k scripts 28k downloads

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

10.32 score 265 stars 1 dependents 900 scripts 9.2k downloads

dotwhisker - Dot-and-Whisker Plots of Regression Results

Create quick and easy dot-and-whisker plots of regression results. It takes as input either (1) a coefficient table in standard form or (2) one (or a list of) fitted model objects (of any type that has methods implemented in the 'parameters' package). It returns 'ggplot' objects that can be further customized using tools from the 'ggplot2' package. The package also includes helper functions for tasks such as rescaling coefficients or relabeling predictor variables. See more methodological discussion of the visualization and data management methods used in this package in Kastellec and Leoni (2007) <doi:10.1017/S1537592707072209> and Gelman (2008) <doi:10.1002/sim.3107>.

Last updated 5 months ago

graphicsplotregression-models

10.17 score 60 stars 656 scripts 2.5k downloads

RcisTarget - RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

Last updated 12 months ago

generegulationmotifannotationtranscriptomicstranscriptiongenesetenrichmentgenetarget

7.93 score 37 stars 191 scripts

SeuratData - 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 1 years ago

datasetssingle-cellsingle-cell-genomics

6.98 score 134 stars 2.0k scripts

penalized - 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 3 years ago

openblascpp

6.87 score 4 stars 16 dependents 429 scripts 1.8k downloads

loupeR - 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 14 days ago

10xgenomicssingle-cell-genomics

5.92 score 107 stars 52 scripts

monocle3 - 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 11 months ago

softwaresinglecellrnaseqatacseqnormalizationpreprocessingdimensionreductionvisualizationqualitycontrolclusteringclassificationannotationgeneexpressiondifferentialexpressionsingle-cell-rna-seqcpp

9.26 score 360 stars 1 dependents 2.2k scripts

BPCells - 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 9 months ago

zlibhdf5cpp

7.03 score 177 stars 174 scripts

speedglm - 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

6.57 score 6 stars 12 dependents 274 scripts 6.3k downloads

Azimuth - 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 1 years ago

shiny-appsingle-cell-genomicssingle-cell-rna-seqcpp

6.37 score 121 stars 434 scripts

DDRTree - Learning Principal Graphs with DDRTree

Project data into a reduced dimensional space and construct a principal graph from the reduced dimension.

Last updated 7 years ago

cpp

5.59 score 5 stars 3 dependents 44 scripts 2.0k downloads

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 2 months ago

5.21 score 40 stars 101 scripts

mdthemes - 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

4.51 score 80 stars 81 scripts 28 downloads

DoubletFinder - DoubletFinder is a suite of tools for identifying doublets in single-cell RNA sequencing data.

DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires (I) Optimal pK selection and (2) Homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies. For more information, see our Cell Sysmtes paper https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30073-0 and our github https://github.com/chris-mcginnis-ucsf/DoubletFinder

Last updated 1 years ago

4.39 score 972 scripts

RforMassSpectrometry - 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 1 years ago

3.93 score 17 stars

blaseRtemplates - 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 7 months ago

2.48 score

muRtools - Mueller's R tools

Fabian's custom plotting functions and utilities

Last updated 4 months ago

1.70 score 1 stars 3 scripts

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 4 months ago

11.56 score 211 stars 13 dependents 786 scripts 2.8k downloads

mhurdle - 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 8 months ago

fortran

3.88 score 15 scripts 610 downloads

genbankr - Parsing GenBank files into semantically useful objects

Reads Genbank files.

Last updated 1 years ago

infrastructuredataimport

4.42 score 17 stars 39 scripts

rdoc - 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 6 years ago

clicolorizationcrayondocumentationpretty-print

4.00 score 49 stars 41 scripts 31 downloads

DAseq - 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 4 years ago

3.81 score 39 stars 33 scripts

GOsummaries - 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 7 years ago

geneexpressionclusteringgovisualizationcpp

3.77 score 11 stars 36 scripts 21 downloads

datascience.curriculum - Data Science 2023

What the package does (one paragraph).

Last updated 2 years ago

3.30 score 1 stars 8 scripts

ChrAccR - 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 2 years ago

2.95 score 18 stars 6 scripts

blaseRdata - Supporting Data for the blaseRtools Package

What the package does (one paragraph).

Last updated 11 months ago

1.70 score 5 scripts

TxDb.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 2 years ago

annotationdatageneticstxdbdanio_rerio

1.70 score

muReportR - muReportR

Generate HTML reports from R. Based on code from the RnBeads package.

Last updated 5 years ago

1.00 score 1 scripts

muLogR - muLogR

Logging and code structuring for R. Based on code from the RnBeads package.

Last updated 6 years ago

1.00 score 1 scripts

ivprobit - Instrumental Variables Probit Model

Compute the instrumental variables probit model using the Amemiya's Generalized Least Squares estimators (Amemiya, Takeshi, (1978) <doi: 10.2307/1911443>).

Last updated 7 years ago

1.00 score 10 scripts 40 downloads