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GitHub topics: bioconductor-package

bridgedb/BridgeDbR Fork of egonw/BridgeDbR

Bioconductor R package for BridgeDb

Language: R - Size: 8.63 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 3

Bioconductor/GenomicFeatures

Query the gene models of a given organism/assembly

Language: R - Size: 45.6 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 27 - Forks: 11

Bioconductor/AnnotationDbi

Manipulation of SQLite-based annotations in Bioconductor

Language: R - Size: 5.36 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 9 - Forks: 10

Al-Murphy/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

Language: R - Size: 9.36 MB - Last synced at: 4 days ago - Pushed at: 19 days ago - Stars: 85 - Forks: 18

Bioconductor/BiocCheck

Language: R - Size: 4.95 MB - Last synced at: 9 days ago - Pushed at: 10 days ago - Stars: 9 - Forks: 27

BIMSBbioinfo/deconvR

The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.

Language: R - Size: 39.8 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 10 - Forks: 3

waldronlab/MultiAssayExperiment

Bioconductor package for management of multi-assay data

Language: R - Size: 5.58 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 73 - Forks: 35

wejlab/TBSignatureProfiler

Profile RNA-seq data using published TB gene signatures

Language: R - Size: 15.6 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 12 - Forks: 12

waldronlab/curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome

Language: R - Size: 176 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 138 - Forks: 32

Bioconductor/GenomicFiles

Distributed computing by file or by range

Language: R - Size: 1 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 2 - Forks: 6

Bioconductor/GenomeInfoDb

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Language: R - Size: 83 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 33 - Forks: 13

lima1/PureCN

Copy number calling and variant classification using targeted short read sequencing

Language: R - Size: 19 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 137 - Forks: 33

rnabioco/raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

Language: C - Size: 22.4 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 8 - Forks: 2

tatami-inc/beachmat

Clone of the Bioconductor repository for the beachmat package.

Language: C++ - Size: 2.12 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 5 - Forks: 5

LTLA/basilisk

Clone of the Bioconductor repository for the basilisk package.

Language: R - Size: 561 KB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 28 - Forks: 13

crisprVerse/crisprScore

On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Language: Python - Size: 80.8 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 20 - Forks: 3

catavallejos/BASiCS

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

Language: R - Size: 90.4 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 84 - Forks: 17

computational-metabolomics/structToolbox

R/Bioconductor package - STRUCT (STatistics in R Using Class Templates) Toolbox: An extensive set of data (pre-)processing and analysis methods and tools for metabolomics and other omics,

Language: R - Size: 30.4 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 10 - Forks: 4

computational-metabolomics/msPurity

A Bioconductor R package - Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Language: HTML - Size: 12.8 MB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 4

Adelia567/Crispr

Crispr is a web app that simplifies the design and analysis of CRISPR guide RNAs, making it accessible for everyone. 🧬 With features like off-target scanning and AI reporting, users can quickly generate and evaluate their gRNA options. 🐙

Language: Python - Size: 158 KB - Last synced at: 30 days ago - Pushed at: 30 days ago - Stars: 0 - Forks: 0

waldronlab/TCGAutils

Toolbox package for organizing and working with TCGA data

Language: R - Size: 688 KB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 28 - Forks: 7

waldronlab/cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

Language: R - Size: 1.12 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 33 - Forks: 14

Bioconductor/BiocParallel

Bioconductor facilities for parallel evaluation

Language: R - Size: 1.27 MB - Last synced at: 7 days ago - Pushed at: 15 days ago - Stars: 68 - Forks: 31

LTLA/csaw

Clone of the Bioconductor repository for the csaw package.

Language: R - Size: 11.3 MB - Last synced at: 6 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 3

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.

Language: R - Size: 462 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 73 - Forks: 20

Bioconductor/BiocStyle

Issues and pull requests for BiocStyle should go here.

Language: R - Size: 588 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 13 - Forks: 20

neurogenomics/MotifPeeker

Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric

Language: R - Size: 7.19 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

CTrierMaansson/DNAfusion

Identification of gene-fusions, including EML4-ALK

Language: R - Size: 63.2 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1

Bioconductor/Organism.dplyr

Language: R - Size: 2.22 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 3

Bioconductor/OrganismDbi

Software to enable the smooth interfacing of different database packages

Language: R - Size: 462 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 2

Bioconductor/txdbmaker

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files)

Language: R - Size: 1.13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1

Bioconductor/BSgenome

Software infrastructure for efficient representation of full genomes and their SNPs

Language: R - Size: 11.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 8

Bioconductor/VariantAnnotation

Annotation of Genetic Variants

Language: R - Size: 3.68 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 28 - Forks: 20

Bioconductor/GenomicAlignments

Representation and manipulation of short genomic alignments

Language: R - Size: 6.09 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 10 - Forks: 15

Bioconductor/SummarizedExperiment

A container (S4 class) for matrix-like assays

Language: R - Size: 1.26 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 35 - Forks: 9

Bioconductor/GenomicRanges

Representation and manipulation of genomic intervals

Language: R - Size: 8.97 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 46 - Forks: 18

Bioconductor/Biostrings

Efficient manipulation of biological strings

Language: R - Size: 30.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 64 - Forks: 17

hemberg-lab/SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

Language: R - Size: 13.5 MB - Last synced at: 22 days ago - Pushed at: about 4 years ago - Stars: 127 - Forks: 55

christinehou11/HuBMAPR

R client to discover and retrieve data on HuBMAP Data Portal

Language: HTML - Size: 5.1 MB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 1

Bioconductor/annotate

Annotation for microarrays

Language: R - Size: 2.46 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 7

Bioconductor/KEGGREST

Client-side REST access to KEGG

Language: R - Size: 128 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 5

Bioconductor/UniProt.ws

R Interface to UniProt Web Services

Language: R - Size: 1.62 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 7 - Forks: 7

crisprVerse/crisprDesign

Comprehensive design of CRISPR gRNAs for nucleases and base editors

Language: R - Size: 5.93 MB - Last synced at: 16 days ago - Pushed at: 5 months ago - Stars: 23 - Forks: 5

MarioniLab/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

Language: R - Size: 608 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 59 - Forks: 28

jackgisby/ReducedExperiment

Containers and tools for dimensionally-reduced -omics data

Language: R - Size: 22.7 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 3 - Forks: 2

HSU-HPC/BERT

Batch-Effect Reduction Trees

Language: R - Size: 165 KB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0

uds-helms/BEclear

Correction of batch effects in DNA methylation data

Language: R - Size: 1.07 MB - Last synced at: 4 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 0

MarioniLab/scran

Clone of the Bioconductor repository for the scran package.

Language: R - Size: 2.89 MB - Last synced at: about 2 months ago - Pushed at: 11 months ago - Stars: 42 - Forks: 22

waldronlab/bugsigdbr

R-side access to published microbial signatures from BugSigDB

Language: R - Size: 422 KB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 3 - Forks: 3

knncolle/BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

Language: R - Size: 753 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 6 - Forks: 11

systemPipeR/systemPipeShiny

A Shiny framework for workflow management and data visualization

Language: R - Size: 26.2 MB - Last synced at: 7 days ago - Pushed at: 2 months ago - Stars: 34 - Forks: 6

LTLA/basilisk.utils

Clone of the Bioconductor repository for the basilisk.utils package.

Language: R - Size: 180 KB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 5

shbrief/GenomicSuperSignature

Interpretation of RNAseq experiments through robust, efficient comparison to public databases

Language: R - Size: 194 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 16 - Forks: 8

waldronlab/VisiumIO

Import spaceranger output and 10X spatial data

Language: R - Size: 1010 KB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

waldronlab/doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets

Language: R - Size: 6.28 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 5 - Forks: 4

saezlab/dorothea

R package to access DoRothEA's regulons

Language: R - Size: 393 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 147 - Forks: 27

neurogenomics/EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

Language: HTML - Size: 30.4 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 17 - Forks: 3

federicomarini/GeneTonic

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

Language: R - Size: 121 MB - Last synced at: 4 days ago - Pushed at: 3 months ago - Stars: 78 - Forks: 11

waldronlab/TENxIO

Bioconductor interface to 10X files

Language: R - Size: 300 KB - Last synced at: 22 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

Language: R - Size: 726 KB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 13 - Forks: 6

waldronlab/CNVRanger

Functionality for CNV analysis

Language: R - Size: 15.9 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 7

waldronlab/HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project

Language: R - Size: 46.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 9 - Forks: 6

waldronlab/SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets

Language: R - Size: 788 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 17 - Forks: 9

waldronlab/curatedTCGAData

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

Language: R - Size: 2.24 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 44 - Forks: 9

waldronlab/curatedOvarianData

The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer

Language: R - Size: 371 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 11 - Forks: 4

kullrich/MSA2dist

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Language: C++ - Size: 616 KB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 0

crisprVerse/crisprViz

Visualization of CRISPR guide RNAs (gRNAs)

Language: R - Size: 1.02 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 0

computational-metabolomics/struct

R/Bioconductor package - STRUCT: STatistics in R Using Class Templates

Language: R - Size: 1.19 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 0

LTLA/BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.

Language: R - Size: 258 KB - Last synced at: 21 days ago - Pushed at: 10 months ago - Stars: 8 - Forks: 3

schifferl/MultimodalExperiment

Integrative Bulk and Single-Cell Experiment Container

Language: R - Size: 2.92 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

schifferl/tuberculosis

Tuberculosis Gene Expression Data for Machine Learning

Language: R - Size: 87.9 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

Bioconductor/DelayedArray

A unified framework for working transparently with on-disk and in-memory array-like datasets

Language: R - Size: 1.35 MB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 27 - Forks: 11

Bioconductor/Rsamtools

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

Language: R - Size: 13.8 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 28 - Forks: 28

waldronlab/terraTCGAdata

TCGA data access on Terra

Language: R - Size: 129 KB - Last synced at: 7 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

waldronlab/MicrobiomeBenchmarkData

Data for benchmarking in microbiome research.

Language: R - Size: 1.34 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

waldronlab/lefser

R implementation of the LEfSe method

Language: R - Size: 18.6 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 58 - Forks: 5

Bioconductor/BSgenomeForge

Forge your own BSgenome data package

Language: R - Size: 202 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 3

Bioconductor/BiocBaseUtils

Language: R - Size: 54.7 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 1

Bioconductor/S4Arrays

Foundation of array-like containers in Bioconductor

Language: R - Size: 459 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 6 - Forks: 1

Bioconductor/HubPub

Language: R - Size: 483 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 4

Bioconductor/BiocIO

Standard input / output framework for use by Bioconductor packages

Language: R - Size: 70.3 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

Bioconductor/BiocSet

Representing Different Biological Sets

Language: R - Size: 395 KB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

Bioconductor/zlibbioc

An R packaged zlib-1.2.5

Language: C - Size: 229 KB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 3

Bioconductor/Rhtslib

HTSlib high-throughput sequencing library as an R package

Language: C - Size: 7.45 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 11 - Forks: 13

Bioconductor/RBGL

An interface to the BOOST graph library

Language: C++ - Size: 27.5 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 7

Bioconductor/Icens

NPMLE for Censored and Truncated Data

Language: R - Size: 75.2 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Bioconductor/hypergraph

A package providing hypergraph data structures

Language: R - Size: 80.1 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

Bioconductor/GSEABase

Gene set enrichment data structures and methods

Language: R - Size: 374 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 12

Bioconductor/graph

graph: A package to handle graph data structures

Language: R - Size: 1.36 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 9

Bioconductor/gpls

Classification using generalized partial least squares

Language: R - Size: 60.5 KB - Last synced at: 19 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

Bioconductor/GOstats

Tools for manipulating GO and microarrays.

Language: TeX - Size: 26 MB - Last synced at: 11 days ago - Pushed at: 4 months ago - Stars: 4 - Forks: 2

Bioconductor/geneplotter

Graphics related functions for Bioconductor

Language: R - Size: 7.32 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 2

Bioconductor/GeneMeta

MetaAnalysis for High Throughput Experiments

Language: R - Size: 30.5 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 3

Bioconductor/genefilter

genefilter: methods for filtering genes from high-throughput experiments

Language: R - Size: 1.15 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 5

Bioconductor/DynDoc

Dynamic document tools

Language: R - Size: 98.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Bioconductor/CoCiteStats

Different test statistics based on co-citation.

Language: R - Size: 56.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1

Bioconductor/chipseq

chipseq: A package for analyzing chipseq data

Language: R - Size: 33.6 MB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 2

Bioconductor/Category

Category Analysis

Language: R - Size: 495 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 2 - Forks: 5

Bioconductor/bioDist

Different distance measures

Language: R - Size: 92.8 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Bioconductor/biocViews

Categorized views of R package repositories

Language: R - Size: 1.51 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 4

Related Keywords
bioconductor-package 190 core-package 64 bioconductor 35 r 25 r-package 17 bioinformatics 15 u24ca289073 15 grna-sequence 9 grna 9 human-cell-atlas 9 sgrna-design 8 grna-sequences 8 crispr-design 8 single-cell-rna-seq 8 crispr 8 machine-learning 7 nci-itcr 7 crispr-cas9 7 crispr-target 7 statistics 7 sgrna 7 genomics 6 crispr-analysis 6 lc-ms 6 metabolomics 6 r01ca230551 5 gene-expression 5 rna-seq 4 dna-methylation 4 dims 4 bioconductor-packages 4 chip-seq 4 experimenthub 4 univariate 3 multivariate-analysis 3 methylation 3 data-visualization 3 shiny 3 causal-inference 2 mass-spectrometry 2 biostatistics 2 targeted-learning 2 rstats 2 isee 2 computational-biology 2 aligner 2 ontologies 2 spatial-transcriptomics 2 visualization 2 transcriptomics 2 gene-set-enrichment 2 workflow 2 high-throughput-sequencing 2 genetics 2 rstudio 2 dimensionality-reduction 2 batch-effect 2 data-integration 2 ribosome-profiling 2 pathway-analysis 2 rpackage 2 systempiper 2 core-services 2 rna-seq-analysis 2 tcga 2 omics 2 genes 2 single-cell 2 logistic-regression 1 loocv 1 normalization 1 r4bioinfo 1 k-means-clustering 1 pca 1 random-forest 1 classification-algorithm 1 k-fold-cross-validation 1 danio-rerio 1 forward-genetics 1 mutation-mapping 1 iseeu 1 cwl 1 adat 1 proteomics 1 proteomics-data-analysis 1 somascan 1 retired-package 1 genome-annotation 1 transcript-model 1 enrichment-analysis 1 gene-sets 1 fun 1 single-cell-methylation 1 wgbs 1 flowsort 1 data 1 blood 1 database 1 single-nucleus-rna-sequencing 1 methylation-analysis 1