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

Apply Mapping Functions in Parallel using Futures

Maftools ⭐ 400

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

Tint is not Tufte

Personal Cancer Genome Reporter (PCGR)

Tools to work with variant call format files

Lambda.r ⭐ 156

Functional programming in R

Gwas_scripts ⭐ 127

Codebook from my GWAS cookbook

Repo for the R package coloc

Superfreq ⭐ 104

Analysis pipeline for cancer sequencing data

Paxos Rs ⭐ 68

Paxos implementation in Rust

Getting Started Bigquery ⭐ 51

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

Cancer Predisposition Sequencing Reporter (CPSR)

Structuralvariantannotation ⭐ 47

R package designed to simplify structural variant analysis

Googlegenomics ⭐ 44

An R package for Google Genomics API queries.

Seqarray ⭐ 41

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

Analysis_pipeline ⭐ 40

TOPMed analysis pipeline

Needlestack ⭐ 39

Multi-sample somatic variant caller

Rstudio Material Theme ⭐ 36

Full RStudio IDE port of the Material Theme

Exac_2015 ⭐ 29

Companion repo for ExAC paper, 2015

Cnv_facets ⭐ 26

Somatic copy variant caller (CNV) for next generation sequencing

Sv_benchmark ⭐ 25

Comprehensive benchmark of structural variant callers

Rsamtools ⭐ 25

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Functions to compare a SV call sets against a truth set.

Ngs Filters ⭐ 25

Filters for false-positive mutation calls in NGS

🧪 Source-controlled split testing stack for building, launching and analysing A/B tests.

1000_genomes_examples ⭐ 23

Examples using R and 1000 genomes data

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

Pledge Rs ⭐ 22

A Rust binding to OpenBSD's pledge(2) interface

Gwas Pipeline ⭐ 20

This is a general (somewhat comprehensive) description of the LNG GWAS pipeline which can be used to guide researchers on how-to run a GWAS.

Gchromvar ⭐ 18

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

Network_snps ⭐ 17

A framework for network analysis and display of SNPs

Crisprvariants ⭐ 17

Fontquiver ⭐ 15

Set of fonts with permissive licences

Driverml ⭐ 14

Miracum Pipe ⭐ 14

Whole exome sequencing pipeline including advanced variant annotation features and automated PDF reporting.

Mito Genotyping ⭐ 13

Repo for scripts for Ludwig et al mtDNA genotyping

Mtb Report ⭐ 12

The user can generate Molecular Tumor Board reports for TCGA samples

Supports de cours de l'Ecole de Bioinformatique Aviesan - IFB - Inserm "Initiation au traitement des données de génomique obtenues par séquençage à haut débit"

VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones.

Frequencyfilter ⭐ 11

Allele frequency filtering for Mendelian variant discovery

Splicing Prediction Pipeline

Signatselect ⭐ 10

signatselect: Identifying signatures of selection

Maf Summary ⭐ 10

Summary of a single or multiple MAF files.

Tissue-specific variant annotation

Gene-based test of allele-specific expression without requiring haplotype information

An efficient genetic data imputation pipeline

Gwas Vcf Specification ⭐ 9

Specification for the GWAS-VCF format (manuscript in preparation)

A tutorial on structural variant calling for short read sequencing data

Multiskat ⭐ 8

MultiSKAT is an R-package focused at rare-variant analysis of continuous multiple phenotype data. This project contains the R-codes/functions (including an example dataset) to carry out the MultiSKAT tests.

Quantumclone ⭐ 8

Clonal reconstruction from HTS data

haploR: utilities for mining Haploreg and other similar web-based tools

Corrcoverage ⭐ 7

Repo for corrcoverage package

Annotatemaf ⭐ 7

Add functional variant annotation to MAF file

R Bindings for htslib/bcf

R package for RIVER (RNA-Informed Variant Effect on Regulation)

An R package for solving maximum-weight connected subrgaph problem and it's variants

Keyholder ⭐ 7

Store Data About Rows

Prnp_penetrance ⭐ 7

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

Simulation of rare and common variants based on 1000 genomes data

TOBI predicts somatic variants from .vcf or .bam input

mitochondrial variant analysis tools

Asimulator ⭐ 6

ASimulatoR: splice-aware RNA-seq data simulation https://doi.org/10.1093/bioinformatics/btab142

Islet_cnn ⭐ 6

Analysis in islet CNN manuscript

Scripts for estimating the age of f2 variants from the paper "Demography and the age of rare variants"

Hmzdelfinder ⭐ 6

CNV calling algorithm for detection of homozygous and hemizygous deletions from whole exome sequencing data

An R package to create a pretty Copy Number Variant plot from a segments file

TreeMap: A Structured Approach to Fine Mapping of eQTL Variants

Tutorials ⭐ 5

bioinformatics tutorials

Treeshapedrearrangements ⭐ 5

Code and data from Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020)

SCANVIS - a toolkit for SCoring, ANnotating and VISualizing splice junctions

visual analysis of your VCF files

A Bioconductor R-package for cell evaluation, characterisation and authentication using high throughput sequencing data.

These scripts reformat a VCF into a SQLite database, with R

Forest plot and funnel plot variants for meta-analysis

Selection Operator for JOintly analyzing multiple variants (SOJO)

Significantly Mutated Region Finder

Wgsaparsr ⭐ 5

Code for parsing TOPMED variant annotation files produced by the WGSA annotation tool.

Viral_variant_caller ⭐ 5

A nextflow pipeline to call single nucleotide and structural variants in viral populations

Clustering somatic mutations to infer intra-tumor heterogeneity 😄

Sqtlseeker2 Nf ⭐ 5

An automated sQTL mapping pipeline using Nextflow

The source code for GERV method

visualization for MaveDB

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