Projects in Awesome Lists tagged with bioconductor

https://github.com/bernatgel/karyoploteR

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

bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r rstats

Last synced: 14 Nov 2024

https://bioinformaticsfmrp.github.io/TCGAbiolinks

TCGAbiolinks

bioc bioconductor gdc integrative-analysis r tcga tcga-data tcgabiolinks

Last synced: 13 Oct 2024

https://github.com/datacamp/rdocumentation-2.0

📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.

bioconductor cran documentation packages rstats

Last synced: 17 Dec 2024

https://github.com/mikelove/bioc-refcard

Bioconductor cheat sheet

bioconductor bioinformatics cheatsheet compbio guide howto microarray r rnaseq

Last synced: 01 Nov 2024

https://github.com/goekelab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 21 Dec 2024

https://github.com/GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 13 Nov 2024

https://github.com/sneumann/xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

bioconductor feature-detection mass-spectrometry metabolomics peak-detection r

Last synced: 19 Dec 2024

https://github.com/stemangiola/tidybulk

Brings bulk and pseudobulk transcriptomics to the tidyverse

bioconductor bulk-transcriptional-analyses deseq2 differential-expression edger ensembl-ids entrez gene-symbols gsea mds-dimensions pca pipe redundancy tibble tidy tidy-data tidyverse transcriptomics transcripts tsne

Last synced: 04 Dec 2024

https://github.com/SingleR-inc/SingleR

Clone of the Bioconductor repository for the SingleR package.

bioconductor singler

Last synced: 04 Dec 2024

https://github.com/Bioconductor/Contributions

Contribute Packages to Bioconductor

bioconductor

Last synced: 16 Nov 2024

https://github.com/bioconductor/contributions

Contribute Packages to Bioconductor

bioconductor

Last synced: 11 Nov 2024

https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

bioconductor jupyter rpy2 scanpy single-cell

Last synced: 15 Dec 2024

https://github.com/lgatto/msnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 20 Dec 2024

https://github.com/lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 12 Nov 2024

https://github.com/Bioconductor/BiocStickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bioconductor stickers

Last synced: 16 Nov 2024

https://github.com/bioconductor/biocstickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bioconductor stickers

Last synced: 21 Dec 2024

https://github.com/mhahsler/rblast

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

bioconductor bioinformatics blast-search

Last synced: 17 Dec 2024

https://github.com/lieberinstitute/spatiallibd

Code for the spatialLIBD R/Bioconductor package and shiny app

10xgenomics bioconductor golem rstats shiny spatial-transcriptomics spatialexperiment spatiallibd visium

Last synced: 16 Dec 2024

https://github.com/bioconductor/genomicdatacommons

Provide R access to the NCI Genomic Data Commons portal.

api-client bioconductor bioinformatics cancer core-services data-science genomics nci r tcga vignette

Last synced: 15 Dec 2024

https://github.com/lgatto/rforproteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

bioconductor bioconductor-packages mass-spectrometry proteomics proteomics-data r tutorial

Last synced: 27 Oct 2024

https://github.com/seandavi/geoquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

bioconductor bioinformatics data-science genomics ncbi-geo r rstats

Last synced: 21 Dec 2024

https://github.com/teunbrand/ggnomics

A small project to add ggplot2 extensions

bioconductor genomics ggplot-extension visualization

Last synced: 27 Oct 2024

https://github.com/federicomarini/genetonic

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

bioconductor bioconductor-package data-exploration data-visualization functional-enrichment-analysis gene-expression gui pathway-analysis r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome transcriptomics user-friendly

Last synced: 20 Dec 2024

https://github.com/neurogenomics/rworkflows

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.

bioconductor containers continuous-integration cran-r docker dockerhub github-actions r reproducibility workflows

Last synced: 13 Nov 2024

https://github.com/bioconductor/bioconductor_docker

Docker Containers for Bioconductor - NEW!

bioconductor bioconductor-containers docker-image

Last synced: 16 Dec 2024

https://github.com/pachterlab/voyager

From geospatial to spatial -omics

bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics

Last synced: 21 Dec 2024

https://github.com/drisso/singlecellexperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

bioconductor bioconductor-package human-cell-atlas single-cell-rna-seq

Last synced: 11 Nov 2024

https://github.com/federicomarini/pcaexplorer

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

bioconductor principal-components r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome user-friendly

Last synced: 18 Dec 2024

https://github.com/lcolladotor/biocthis

Automate package and project setup for Bioconductor packages

actions bioconductor biocthis github rstats styler usethis

Last synced: 18 Dec 2024

https://saezlab.github.io/misty

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 14 Dec 2024

https://saezlab.github.io/mistyR/

Multiview Intercellular SpaTial modeling framework

bioconductor biology intercellular machine-learning modular molecular-biology multiview r spatial spatial-transcriptomics

Last synced: 12 Nov 2024

https://github.com/lcolladotor/derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

annotation-agnostic bioconductor derfinder r rnaseq rstats

Last synced: 18 Dec 2024

https://github.com/plger/pipecomp

A R framework for pipeline benchmarking, with application to single-cell RNAseq

benchmark bioconductor clustering pipeline-benchmarking pipelines single-cell-rna-seq

Last synced: 09 Nov 2024

https://github.com/lmweber/principlessta

"Principles of Spatial Transcriptomics Analysis with Bioconductor" book

analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 13 Dec 2024

https://github.com/bioinformatics-core-shared-training/ngs-in-bioc

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

bioconductor ngs rna-seq training

Last synced: 03 Nov 2024

https://github.com/grimbough/biomart

R package providing query functionality to BioMart instances like Ensembl

bioconductor biomart ensembl r

Last synced: 17 Dec 2024

https://github.com/nanxstats/rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

bioconductor bioinformatics cheminformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

Last synced: 20 Dec 2024

https://github.com/rformassspectrometry/spectra

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 20 Dec 2024

https://rformassspectrometry.github.io/Spectra/

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 07 Nov 2024

https://github.com/biogenies/tidysq

tidy processing of biological sequences in R

bioconductor bioinformatics biological-sequences fasta r rstats s3 sequences tibble tidy tidyverse vctrs

Last synced: 19 Nov 2024

https://github.com/systemPipeR/systemPipeShiny

A Shiny framework for workflow management and data visualization

bioconductor bioconductor-package data-visualization r shiny systempiper

Last synced: 04 Dec 2024

https://github.com/jorainer/ensembldb

This is the ensembldb development repository.

annotation bioconductor bioconductor-packages ensembl

Last synced: 20 Dec 2024

https://github.com/lieberinstitute/recount3

Explore and download data from the recount3 project

annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse r recount recount3 rnaseq rstats

Last synced: 30 Nov 2024

https://github.com/federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

bioconductor differential-expression r reproducible-research rna-seq rna-seq-analysis shiny user-friendly

Last synced: 16 Dec 2024

https://github.com/bodenmillergroup/imcdataanalysis

R based workflow for multiplexed imaging data

bioconductor image-analysis single-cell spatial-analysis

Last synced: 09 Nov 2024

https://github.com/nullranges/nullranges

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one or more covariates (matchRanges).

bioconductor bootstrap genomics matching statistics

Last synced: 12 Oct 2024

https://github.com/bioconductor/bioconductor_full

DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages

bioconductor containers docker

Last synced: 11 Nov 2024

https://rformassspectrometry.github.io/QFeatures/

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 07 Nov 2024

https://github.com/Polkas/pacs

Supplementary R packages utils

bioconductor cran dependencies library lifeduration r r-package renv shiny tools utils

Last synced: 04 Dec 2024

https://github.com/rformassspectrometry/qfeatures

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 16 Dec 2024

https://github.com/mikelove/alpine

Modeling and correcting fragment sequence bias for RNA-seq

bioconductor rnaseq

Last synced: 27 Oct 2024

https://github.com/bioconductor/bioconductor.org

Source code for the Bioconductor website

bioconductor website

Last synced: 11 Nov 2024

https://github.com/ltla/scrnaseq

Clone of the Bioconductor repository for the scRNAseq package.

bioconductor

Last synced: 30 Oct 2024

https://github.com/lpantano/degreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

bioconductor differential-expression qc r report rna-seq smallrna

Last synced: 27 Oct 2024

https://github.com/aoles/rbioformats

:books: R interface to the Bio-Formats library

bio-formats bioconductor image-processing r

Last synced: 31 Oct 2024

https://github.com/mikelove/deseq2_or_edger

DESeq2 or edgeR

bioconductor deseq2 rnaseq

Last synced: 12 Oct 2024

https://github.com/seandavi/biocpkgtools

Computable build reports, package metadata, and download stats from the Bioconductor project

bioconductor metadata rstats

Last synced: 17 Dec 2024

https://github.com/Appsilon/shiny.gosling

R Shiny wrapper for Gosling.js - Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization

bioconductor genomics-visualization r shiny

Last synced: 27 Nov 2024

https://github.com/darwinawardwinner/cd4-csaw

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

bioconductor bioinformatics-pipeline chip-seq r reproducible-research rna-seq

Last synced: 08 Nov 2024

https://rformassspectrometry.github.io/MsCoreUtils/

Core Utils for Mass Spectrometry Data

bioconductor mass-spectrometry metabolomics proteomics rstats utils

Last synced: 07 Nov 2024

https://github.com/rformassspectrometry/mscoreutils

Core Utils for Mass Spectrometry Data

bioconductor mass-spectrometry metabolomics proteomics rstats utils

Last synced: 16 Dec 2024

https://github.com/lieberinstitute/spatialdlpfc

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

bioconductor dlpfc rstats spatial-transcriptomics spatialdlpfc transcriptomics visium visium-spg

Last synced: 30 Nov 2024

https://github.com/lgatto/proloc

A unifying bioinformatics framework for organelle proteomics

bioconductor proteomics proteomics-data r spatial-proteomics visualisation

Last synced: 16 Dec 2024

https://github.com/Marlin-Na/TnT

Interactive visulizations for track-based genomic data in R

bioconductor genome-browser htmlwidgets r shiny

Last synced: 15 Nov 2024

https://github.com/marlin-na/tnt

Interactive visulizations for track-based genomic data in R

bioconductor genome-browser htmlwidgets r shiny

Last synced: 19 Dec 2024

https://github.com/bioconductor/bioc_git_transition

This python package is for transitioning bioconductor from SVN to git

bioconductor git svn2git

Last synced: 11 Nov 2024

https://github.com/cbg-ethz/dce

Finding the causality in biological pathways

bioconductor causality r

Last synced: 17 Nov 2024

https://github.com/philboileau/scpca

A toolbox for sparse contrastive principal component analysis

bioconductor contrastive-learning dimensionality-reduction

Last synced: 16 Dec 2024

https://github.com/grimbough/bioc-actions

GitHub Actions for developing and maintaining Bioconductor packages

bioconductor github-actions r r-programming rcmdcheck software-testing

Last synced: 08 Nov 2024

https://github.com/matthewcarlucci/discorhythm

An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface

bioconductor data-visualization oscillations package r rhythm-detection webapp

Last synced: 28 Oct 2024

https://github.com/rformassspectrometry/rformassspectrometry.org

The R for Mass Spectrometry Initiative home page

bioconductor mass-spectrometry rstats

Last synced: 16 Nov 2024

https://github.com/ropensci/baseset

Provides classes for working with sets

bioconductor bioconductor-package package r r-package sets

Last synced: 08 Nov 2024

https://bernatgel.github.io/karyoploter_tutorial/

Examples on how to use the karyoploteR R/Bioconductor package

bioconductor bioinformatics data-visualization genomics-visualization plotting-in-r rstats tutorial

Last synced: 20 Nov 2024

https://github.com/kevinrue/biocchallenges

Challenges for the Biocoductor community.

bioconductor bioconductor-package challenges community-driven

Last synced: 30 Oct 2024

https://github.com/kevinrue/goexpress

Analysies of gene expression data using Gene Ontology

bioconductor bioconductor-package bioconductor-stats geneontology geneset-enrichment

Last synced: 30 Oct 2024

https://github.com/nanxstats/dockflow

Containerize Bioconductor Workflows

bioconductor bioinformatics containerization docker workflow

Last synced: 16 Nov 2024

https://github.com/federicomarini/hcadata

Access data from the Human Cell Atlas project, directly via R/Bioconductor

bioconductor dataset experimenthub human-cell-atlas rna-seq single-cell-rna-seq

Last synced: 16 Oct 2024

https://github.com/lpantano/isomirs

analyze isomiRs from seqbuster tool

analyze-isomirs bioconductor isomirs mirna r

Last synced: 27 Oct 2024

https://github.com/goekelab/nanoporernaseq

Nanopore RNASeq data

bioconductor long-reads nanopore r rna-seq sg-nex

Last synced: 09 Nov 2024

https://github.com/lieberinstitute/recountworkshop2020

BioC2020 workshop: Human RNA-seq data from recount2 and related packages

bioc2020 bioconductor derfinder genomicstate recount recount-brain recount2 rstats workshop

Last synced: 30 Nov 2024

https://github.com/bioconductor/hcabrowser

Browse the Human Cell Atlas data portal

bioconductor human-cell-atlas

Last synced: 11 Nov 2024

https://github.com/bioconductor/eurobioc2017

European Bioconductor Meeting 2017

bioconductor conference r

Last synced: 11 Nov 2024

https://github.com/bioconductor/biocworkinggroups

Bioconductor working group guidelines. Also, a list of active, suggested, and inactive working groups for bioconductor for the community to volunteer to be apart of. The community is also welcome to suggest new working groups.

bioconductor book community guidelines working-group

Last synced: 11 Nov 2024