Awesome Open Source

Programming Languages

Search results for r genome

193 search results found

Karyoploter ⭐ 278

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Personal Cancer Genome Reporter (PCGR)

Ngsplot ⭐ 231

Quick mining and visualization of NGS data by integrating genomic databases

Smudgeplot ⭐ 200

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Biomartr ⭐ 198

Genomic Data Retrieval with R

Genvisr ⭐ 188

Genome data visualizations

Methylkit ⭐ 176

R package for DNA methylation analysis

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Sigminer ⭐ 119

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/

Plyranges ⭐ 103

A grammar of genomic data transformation

mgatk: mitochondrial genome analysis toolkit

treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes

Genome Interval Arithmetic in R

Gwasrapidd ⭐ 78

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data

Ichorcna ⭐ 73

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Rideogram ⭐ 72

R/qtl: A QTL mapping environment

Orthologr ⭐ 68

Genome wide orthology inference and dNdS estimation

Titancna ⭐ 59

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

Automatic DNA methylation detection from nanopore tools and their consensus model

An accurate and ultra-fast hybrid genome assembler

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2

Visualization and annotation of CNVs from population-scale whole-genome sequencing data

dcHiC: Differential compartment analysis for Hi-C datasets

GENome Organisation Visual Analytics

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

Seqarray ⭐ 41

Data management of large-scale whole-genome sequence variant calls (Development version only)

Crisprcleanr ⭐ 41

Unsupervised correction of gene independent cell responses to CRISPR-cas9

Agnostos Wf ⭐ 39

Get_phylomarkers ⭐ 39

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

Curatedtcgadata ⭐ 38

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Shinychromosome ⭐ 38

an R/Shiny application for interactive creation of non-circular plots of whole genomes

Gtrellis ⭐ 36

Genomic plot in trellis layout

Nam Genomes ⭐ 34

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

QDNAseq package for Bioconductor

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

Pmsignature ⭐ 32

R package for extracting mutation signatures from a list of somatic mutations

De novo annotation of young retrotransposons

Proactiv ⭐ 29

Estimation of Promoter Activity from RNA-Seq data

Full-spectrum copy number variation detection by high-throughput DNA sequencing

Shallowhrd ⭐ 28

This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination Deficiency of a tumor based on the number of Large-scale Genomic Alterations (LGAs).

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

Gwasglue ⭐ 28

Linking GWAS data to analytical tools in R

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

Metablastr ⭐ 27

Seamless Integration of BLAST Sequence Searches in R

Deepstats ⭐ 27

deepStats: a stastitical toolbox for deeptools and genomic signals

Gwaspipeline ⭐ 26

Mcpcounter ⭐ 26

Analysing Metagenomic Species (MGS)

Readdepth ⭐ 24

R package for inferring copy number from read depth

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

Motifbreakr ⭐ 24

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.

Abbreviate strings to short, unique identifiers

1000_genomes_examples ⭐ 23

Examples using R and 1000 genomes data

Heterogeneity ⭐ 23

Code accompanying Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Aceseqworkflow ⭐ 22

Allele-specific copy number estimation with whole genome sequencing

Copy Number Analysis ⭐ 22

Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Biosequtils ⭐ 21

Extract Sequence from Genome According to Annotation File

Proxysnps ⭐ 21

🔖 Get SNP proxies from the 1000 Genomes Project.

Echolocator ⭐ 20

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Expanded STR algorithm for Illumina sequencing data

Tcgautils ⭐ 20

Toolbox package for organizing and working with TCGA data

Liftoverplink ⭐ 20

A wrapper for liftOver for converting plink genotype data between different genome reference builds

Reduce + Visualize Gene Ontology

Findmyfriends ⭐ 19

Fast alignment-free pangenome creation and exploration

Lcwgs Guide Tutorial ⭐ 19

Linked Selection ⭐ 19

Gwaspoly ⭐ 18

GWAS software that can handle autopolyploids

Exorthist ⭐ 18

ExOrthist: a pipeline to extract exon orthologies at any evolutionary distance.

Viral Track ⭐ 18

4C-seq processing pipeline

Genetic Data Analysis 2 ⭐ 17

RCC workshop, "Analysis of Genetic Data 2: Mapping Genome-wide Associations."

Sigprofilermatrixgeneratorr ⭐ 17

R wrapper for utilizing the SigProfilerMatrixGenerator framework

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Motifmatchr ⭐ 17

Fast motif matching in R

Cn_learn ⭐ 17

Micropro ⭐ 17

A microbial profiling framework for metagenomic analysis

Chipseqspikeinfree ⭐ 16

A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

Genemates ⭐ 16

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences

Graph-aware Retrieval of Selective Sweeps

Informme ⭐ 15

An information-theoretic pipeline for methylation analysis of WGBS data

Repository for R package MetQy (read related publication here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC62479

Millefy: Genome browser-like visualization of single-cell RNA-seq dataset

Read, manipulate and visualize 'Pairwise mApping Format' data in R

Targetscantools ⭐ 14

A suite of tools for evolutionary and functional analysis of microRNA binding sites http://www.targetscan.org

Diff_splice_paper ⭐ 14

Code for differential splicing comparison paper (Soneson, Matthes, et al.)

Driverml ⭐ 14

Methylsig ⭐ 14

R package for DNA methylation analysis

Easy Copy Number !

Tcga_ab_compartments ⭐ 13

A/B compartments for 12 cancer types estimated from TCGA methylation data

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

Genomeqc ⭐ 12

Scapatrap ⭐ 12

Related Searches

R Rstats (2,342)

R Rstudio (1,746)

Python Genome (1,622)

R Dataset (1,493)

Python R (1,244)

R Machine Learning (1,113)

R Visualization (979)

1-100 of 193 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.