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Search results for r genomics

134 search results found

Seurat ⭐ 2,025

R toolkit for single cell genomics

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

Gggenomes ⭐ 518

A grammar of graphics for comparative genomics

Scrna Seq_notes ⭐ 478

A list of scRNA-seq analysis tools

Maftools ⭐ 400

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

Canvasxpress ⭐ 282

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

Tools to work with variant call format files

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Biomartr ⭐ 198

Genomic Data Retrieval with R

Gwa_tutorial ⭐ 184

A comprehensive tutorial about GWAS and PRS

Genomics ⭐ 154

A collection of scripts and notes related to genomics and bioinformatics

Gene set variation analysis

An R package for creating Q-Q and manhattan plots from GWAS results

Mixomics ⭐ 126

Development repository for the Bioconductor package 'mixOmics '

Omicsplayground ⭐ 112

Visual self-service analytics platform for big omics data.

mgatk: mitochondrial genome analysis toolkit

Genomicdatacommons ⭐ 80

Provide R access to the NCI Genomic Data Commons portal.

Geoquery ⭐ 73

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Ggnomics ⭐ 69

A small project to add ggplot2 extensions

Orthologr ⭐ 68

Genome wide orthology inference and dNdS estimation

Multiassayexperiment ⭐ 67

Bioconductor package for management of multi-assay data

Titancna ⭐ 59

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer

Mungesumstats ⭐ 59

Rapid standardisation and quality control of GWAS or QTL summary statistics

Palimpsest ⭐ 56

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.

MSigDB gene sets for multiple organisms in a tidy data format

Getting Started Bigquery ⭐ 51

Examples of how to get started with genomics data in BigQuery in many languages.

Magma_celltyping ⭐ 50

Find causal cell-types underlying complex trait genetics

Googlegenomics ⭐ 44

An R package for Google Genomics API queries.

PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.

Get_phylomarkers ⭐ 39

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Alphasimr ⭐ 36

R package for breeding program simulations

Shiny Iatlas ⭐ 36

An interactive web portal for exploring immuno-oncology data

🐳 Genomics Research Container Architecture

Nam Genomes ⭐ 34

Detailed bioinformatics scripts and methods used in the NAM genome paper.

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Sscclust ⭐ 32

simpler single cell RNAseq data clustering

Read specialized NGS formats as data frames in R, Python, and more.

Orthogene ⭐ 31

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

Jbrowser ⭐ 31

R interface to the JBrowse 2 Linear Genome View.

A Suite of Packages for Analysis of Big Genomic Data

Proactiv ⭐ 29

Estimation of Promoter Activity from RNA-Seq data

Cbioportaldata ⭐ 29

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

Wiggleplotr ⭐ 28

A small R package to make sequencing read coverage plots in R.

Phylostratr ⭐ 28

An R framework for phylostratigraphy

Sevenbridges R ⭐ 27

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

Deepstats ⭐ 27

deepStats: a stastitical toolbox for deeptools and genomic signals

Compgenr ⭐ 26

Package to wrangle and visualize genomic data in R

DeepG, or 'Deep Genomics', is a R library which allows to train and apply deep neural networks on genomic datasets

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Nullranges ⭐ 23

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or set of control ranges that are matched across one or more covariates.

Discover ⭐ 23

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

Omicnavigator ⭐ 21

Open-Source Software for Omic Data Analysis and Visualization

R_docker ⭐ 19

Docker container for genomics analyses in R.

Netsmooth ⭐ 18

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)

Gdscic50 ⭐ 18

An R package to fit dose response curves for data from the Genomics of Drug Sensitivity of Cancer (GDSC) project.

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

Interminer ⭐ 17

R package for InterMine

Muto_wilson_ncomm_2020 ⭐ 17

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

Ctdnatools ⭐ 17

R package to work with ctDNA sequencing data

stackr: an R package to run stacks software pipeline

Granatum ⭐ 17

Graphsim ⭐ 16

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

R Outbreak Info ⭐ 16

R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.

Switchde ⭐ 15

Inference of switch-like differential expression along single-cell trajectories

Biocancer ⭐ 15

♋ 🆓 A Shiny App for Interactive Multi-OMICS Cancer Data Visualization and analysis

Dropclust ⭐ 15

Version 2.1.0 released

Prioritizing Cancer Driver Genes Using Genomics Data

Cellrangerrkit ⭐ 14

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Clustassess ⭐ 13

Tools for assessing clustering robustness

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

Machine learning algorithm to predict biological pathway relationships based on functional genomics networks

Assigner ⭐ 12

Population assignment analysis using R

Analysing Capture Seq Count Data

CNAqc - Copy Number Alteration (CNA) Quality Check package

1000 Genomes Project Metadata R Package

North_american_vitis_pangenome ⭐ 12

Construct and Analyze the North American Vitis pangenome

Tenxbrainanalysis ⭐ 12

R scripts for analyzing the 1.3 million brain cell data set from 10X Genomics

Cellector ⭐ 11

Macrosyntr ⭐ 11

R package for comparison of synteny conservation at the genome-wide scale.

Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data

Plot_genome_align_fig ⭐ 10

Plot genome alignment figure using progressiveMauve & genoPlotR

Three bacterial GWAS methods all rolled into one easy-to-use R package

This project proposes to contribute to fill the knowledge gap about Covid-19SARS-CoV-2 in Brazil and with the global knowledge about the pathogen. The scientific community and governments of other countries are looking for actions along these lines. The United Kingdom recently established a research network for genomic studies of SARS-CoV-2Covid-19 with a contribution of GBP 20 million (https://www.gov.uk/government/news/uk-launches-wh genome-sequence-alliance-to-map-spread-of-coronavi

Scrna_seq ⭐ 10

scRNA seq analysis using Seurat V3

Bedmatrix ⭐ 10

A matrix-like wrapper around PLINK .bed files

Metaomics ⭐ 10

Shiny GUI application for genomics meta-analysis

Workshop Tidyverse ⭐ 9

Workshop: Using R/tidyverse to analyze & visualize gapminder/processed transcriptomics data!

Bioconcotk ⭐ 9

Bioconductor components for general cancer genomics

📚 Genomics Platform Group Reporter

Singlecell ⭐ 8

Screclassify ⭐ 8

Post hoc cell type classification of single-cell RNA-sequencing data.

Quantumclone ⭐ 8

Clonal reconstruction from HTS data

Tidyomics ⭐ 8

Easily install and load packages from the tidyomcis ecosystem

Winterschool.2016 ⭐ 7

Repository for Winter School 2016- Bioinformatics for Adaptation Genomics

Bioinfohub ⭐ 7

R Client for Seven Bridges Genomics API (v1)

Scrattch.io ⭐ 7

Functions for handling RNA-seq files and formats as input and output for scrattch functions.

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