HSU-HPC/BERT

Batch-Effect Reduction Trees

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Bioconductor/GenomicFeatures

Query the gene models of a given organism/assembly

Language: R - Size: 45.6 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 27 - Forks: 11

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: 1.12 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 3 - Forks: 1

MarioniLab/scran

Clone of the Bioconductor repository for the scran package.

Language: R - Size: 2.89 MB - Last synced at: 1 day ago - Pushed at: 9 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: 9 days ago - Pushed at: 9 days ago - Stars: 3 - Forks: 3

MarioniLab/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

Language: R - Size: 605 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 58 - Forks: 28

Bioconductor/BiocParallel

Bioconductor facilities for parallel evaluation

Language: R - Size: 1.26 MB - Last synced at: 4 days ago - Pushed at: 10 days ago - Stars: 67 - Forks: 31

Bioconductor/UniProt.ws

R Interface to UniProt Web Services

Language: R - Size: 1.62 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 5 - Forks: 7

Bioconductor/GenomeInfoDb

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

Language: R - Size: 83 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 33 - Forks: 13

Bioconductor/Biostrings

Efficient manipulation of biological strings

Language: R - Size: 30.3 MB - Last synced at: 12 days ago - Pushed at: 30 days ago - Stars: 64 - Forks: 17

knncolle/BiocNeighbors

Clone of the Bioconductor repository for the BiocNeighbors package.

Language: R - Size: 753 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 6 - Forks: 11

waldronlab/curatedMetagenomicData

Curated Metagenomic Data of the Human Microbiome

Language: R - Size: 176 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 133 - Forks: 32

systemPipeR/systemPipeShiny

A Shiny framework for workflow management and data visualization

Language: R - Size: 26.2 MB - Last synced at: 3 days ago - Pushed at: 19 days ago - Stars: 34 - Forks: 6

LTLA/basilisk

Clone of the Bioconductor repository for the basilisk package.

Language: R - Size: 561 KB - Last synced at: 3 days ago - Pushed at: 19 days ago - Stars: 27 - Forks: 14

crisprVerse/crisprScore

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

Language: Python - Size: 80.8 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 20 - Forks: 4

LTLA/basilisk.utils

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

Language: R - Size: 177 KB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 5

Al-Murphy/MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

Language: R - Size: 9.24 MB - Last synced at: 13 days ago - Pushed at: about 2 months ago - Stars: 81 - Forks: 17

Bioconductor/BiocCheck

Language: R - Size: 4.92 MB - Last synced at: 14 days ago - Pushed at: 23 days ago - Stars: 8 - Forks: 27

shbrief/GenomicSuperSignature

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

Language: R - Size: 194 MB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 16 - Forks: 7

Bioconductor/GenomicFiles

Distributed computing by file or by range

Language: R - Size: 1020 KB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 2 - Forks: 6

CTrierMaansson/DNAfusion

Identification of gene-fusions, including EML4-ALK

Language: R - Size: 63.2 MB - Last synced at: 16 days ago - Pushed at: 25 days ago - Stars: 3 - Forks: 1

waldronlab/doppelgangR

Identify possibly duplicate samples in a list of ExpressionSets

Language: R - Size: 6.28 MB - Last synced at: 16 days ago - Pushed at: 26 days ago - Stars: 5 - Forks: 4

saezlab/dorothea

R package to access DoRothEA's regulons

Language: R - Size: 393 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 147 - Forks: 27

Bioconductor/OrganismDbi

Software to enable the smooth interfacing of different database packages

Language: R - Size: 443 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 2

neurogenomics/EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

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federicomarini/GeneTonic

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

Language: R - Size: 121 MB - Last synced at: 15 days ago - Pushed at: 29 days ago - Stars: 78 - Forks: 10

Bioconductor/GenomicRanges

Representation and manipulation of genomic intervals

Language: R - Size: 8.97 MB - Last synced at: 10 days ago - Pushed at: about 2 months ago - Stars: 46 - Forks: 18

waldronlab/GSEABenchmarkeR

Reproducible GSEA Benchmarking

Language: R - Size: 723 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 13 - Forks: 5

waldronlab/CNVRanger

Functionality for CNV analysis

Language: R - Size: 15.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 8 - Forks: 7

waldronlab/VisiumIO

Import spaceranger output and 10X spatial data

Language: R - Size: 1010 KB - Last synced at: 26 days ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

waldronlab/TENxIO

Bioconductor interface to 10X files

Language: R - Size: 296 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

waldronlab/cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment

Language: R - Size: 1.27 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 33 - Forks: 13

waldronlab/HMP16SData

16S rRNA Sequencing Data from the Human Microbiome Project

Language: R - Size: 46.6 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 6

waldronlab/TCGAutils

Toolbox package for organizing and working with TCGA data

Language: R - Size: 652 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 27 - Forks: 7

waldronlab/SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets

Language: R - Size: 788 KB - Last synced at: about 1 month ago - Pushed at: about 1 month 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 44 - Forks: 9

waldronlab/MultiAssayExperiment

Bioconductor package for management of multi-assay data

Language: R - Size: 5.56 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 72 - Forks: 34

waldronlab/curatedOvarianData

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

Language: R - Size: 371 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 4

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: 461 KB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 72 - Forks: 20

tatami-inc/beachmat

Clone of the Bioconductor repository for the beachmat package.

Language: C++ - Size: 2.1 MB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 5 - Forks: 5

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: 615 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

wejlab/TBSignatureProfiler

Profile RNA-seq data using published TB gene signatures

Language: R - Size: 15.6 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 12 - Forks: 12

jackgisby/ReducedExperiment

Containers and tools for dimensionally-reduced -omics data

Language: R - Size: 22.3 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 4 - Forks: 1

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

crisprVerse/crisprViz

Visualization of CRISPR guide RNAs (gRNAs)

Language: R - Size: 1.02 MB - Last synced at: 10 days ago - Pushed at: about 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: about 1 month ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0

lima1/PureCN

Copy number calling and variant classification using targeted short read sequencing

Language: R - Size: 19 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 134 - Forks: 33

LTLA/BiocSingular

Clone of the Bioconductor repository for the BiocSingular package.

Language: R - Size: 258 KB - Last synced at: 28 days ago - Pushed at: 9 months ago - Stars: 8 - Forks: 3

schifferl/MultimodalExperiment

Integrative Bulk and Single-Cell Experiment Container

Language: R - Size: 2.92 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

schifferl/tuberculosis

Tuberculosis Gene Expression Data for Machine Learning

Language: R - Size: 87.9 KB - Last synced at: about 2 months ago - Pushed at: about 2 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: 1.62 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 27 - Forks: 9

Bioconductor/Rsamtools

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

Language: R - Size: 13.8 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 28 - Forks: 28

waldronlab/terraTCGAdata

TCGA data access on Terra

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waldronlab/MicrobiomeBenchmarkData

Data for benchmarking in microbiome research.

Language: R - Size: 1.34 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

waldronlab/lefser

R implementation of the LEfSe method

Language: R - Size: 18.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 58 - Forks: 5

Bioconductor/BSgenomeForge

Forge your own BSgenome data package

Language: R - Size: 202 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 3

Bioconductor/BiocBaseUtils

Language: R - Size: 54.7 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 1

Bioconductor/S4Arrays

Foundation of array-like containers in Bioconductor

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Bioconductor/HubPub

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Bioconductor/BiocIO

Standard input / output framework for use by Bioconductor packages

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Bioconductor/BiocSet

Representing Different Biological Sets

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Bioconductor/zlibbioc

An R packaged zlib-1.2.5

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Bioconductor/VariantAnnotation

Annotation of Genetic Variants

Language: R - Size: 3.68 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 28 - Forks: 20

Bioconductor/Rhtslib

HTSlib high-throughput sequencing library as an R package

Language: C - Size: 7.45 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 11 - Forks: 13

Bioconductor/RBGL

An interface to the BOOST graph library

Language: C++ - Size: 27.5 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 7

Bioconductor/KEGGREST

Client-side REST access to KEGG

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Bioconductor/Icens

NPMLE for Censored and Truncated Data

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Bioconductor/hypergraph

A package providing hypergraph data structures

Language: R - Size: 80.1 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

Bioconductor/GSEABase

Gene set enrichment data structures and methods

Language: R - Size: 374 KB - Last synced at: about 1 month ago - Pushed at: about 2 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: about 1 month ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 9

Bioconductor/gpls

Classification using generalized partial least squares

Language: R - Size: 60.5 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

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 2 months ago - Stars: 10 - Forks: 15

Bioconductor/geneplotter

Graphics related functions for Bioconductor

Language: R - Size: 7.32 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 2

Bioconductor/GeneMeta

MetaAnalysis for High Throughput Experiments

Language: R - Size: 30.5 MB - Last synced at: about 1 month ago - Pushed at: about 2 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: about 1 month ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 5

Bioconductor/DynDoc

Dynamic document tools

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Bioconductor/CoCiteStats

Different test statistics based on co-citation.

Language: R - Size: 56.6 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

Bioconductor/chipseq

chipseq: A package for analyzing chipseq data

Language: R - Size: 33.6 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 2

Bioconductor/Category

Category Analysis

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Bioconductor/bioDist

Different distance measures

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Bioconductor/biocViews

Categorized views of R package repositories

Language: R - Size: 1.51 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 4 - Forks: 4

Bioconductor/Biobase

Biobase: Base functions for Bioconductor

Language: R - Size: 5.62 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 10

Bioconductor/AnnotationForge

Tools for building SQLite-based annotation data packages

Language: R - Size: 25.1 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 9

Bioconductor/AnnotationDbi

Manipulation of SQLite-based annotations in Bioconductor

Language: R - Size: 5.36 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 10

Bioconductor/annotate

Annotation for microarrays

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Bioconductor/ShortRead

Language: R - Size: 7.14 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 6

Bioconductor/ExperimentHubData

Add resources to ExperimentHub

Language: R - Size: 344 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 5

Bioconductor/IRanges

Foundation of integer range manipulation in Bioconductor

Language: R - Size: 4.29 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 11

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 2 months ago - Stars: 9 - Forks: 8

Bioconductor/S4Vectors

Foundation of vector-like and list-like containers in Bioconductor

Language: R - Size: 1.44 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 22

Bioconductor/SplicingGraphs

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Language: R - Size: 144 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 1

Bioconductor/HDF5Array

HDF5 datasets as array-like objects in R

Language: R - Size: 8.69 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 14

Bioconductor/XVector

Foundation of external vector representation and manipulation in Bioconductor

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Bioconductor/BiocGenerics

Defines many S4 generic functions used in Bioconductor

Language: R - Size: 337 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 9

Bioconductor/AnnotationFilter

Facilities for Filtering Bioconductor Annotation Resources

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Bioconductor/Organism.dplyr

Language: R - Size: 2.21 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 3

Bioconductor/BiocStyle

Issues and pull requests for BiocStyle should go here.

Language: R - Size: 572 KB - Last synced at: 21 days ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 20

Bioconductor/MatrixGenerics

S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects

Language: R - Size: 384 KB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 12 - Forks: 1

Bioconductor/BiocVersion

Size: 19.5 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

Bioconductor/SparseArray

High-performance sparse data representation and manipulation in R

Language: C - Size: 1 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 9 - Forks: 2