Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "DataImport" keyword

ExperimentHubData 1.28.0
Add resources to ExperimentHub
3 versions - Latest release: 6 months ago - 3 dependent packages - 27.5 thousand downloads total - 1 maintainer
TPP2D 1.18.0
Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
3 versions - Latest release: 6 months ago - 5.21 thousand downloads total - 1 maintainer
ReUseData 1.2.2
Reusable and reproducible Data Management
5 versions - Latest release: 5 months ago - 1.11 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)
3 versions - Latest release: 21 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
Rsamtools 2.20.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
3 versions - Latest release: 21 days ago - 212 dependent packages - 3.91 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: 21 days ago - 96 dependent packages - 622 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.72.0
Efficient manipulation of biological strings
6 versions - Latest release: 21 days ago - 333 dependent packages - 6.29 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.12.0
an R package for visualization of tree and annotation data
4 versions - Latest release: 21 days ago - 28 dependent packages - 1.15 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 21 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.32.0
HDF5 backend for DelayedArray objects
4 versions - Latest release: 21 days ago - 54 dependent packages - 990 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.62.0
FASTQ input and manipulation
3 versions - Latest release: 21 days ago - 36 dependent packages - 1.63 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.40.0
Representation and manipulation of short genomic alignments
5 versions - Latest release: 21 days ago - 132 dependent packages - 3.57 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.26.0
S4 Classes for Single Cell Data
3 versions - Latest release: 21 days ago - 201 dependent packages - 1.07 million downloads total - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.64.0
R interface to genome annotation files and the UCSC genome browser
3 versions - Latest release: 21 days ago - 251 dependent packages - 3.87 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.50.0
Annotation of Genetic Variants
4 versions - Latest release: 21 days ago - 93 dependent packages - 1.55 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.48.0
R Interface to HDF5
4 versions - Latest release: 21 days ago - 69 dependent packages - 2.09 million downloads total - 59 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis
3 versions - Latest release: 6 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
MDTS 1.22.0
Detection of de novo deletion in targeted sequencing trios
3 versions - Latest release: 6 months ago - 7.04 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 16 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.12.0
Microbiome analysis
3 versions - Latest release: 22 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.34.0
Nucleosome positioning package for R
3 versions - Latest release: 6 months ago - 27.2 thousand downloads total - 1 maintainer
aCGH 1.80.0
Classes and functions for Array Comparative Genomic Hybridization data
3 versions - Latest release: 6 months ago - 5 dependent packages - 62.7 thousand downloads total - 1 maintainer
MsBackendMgf 1.10.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
3 versions - Latest release: 6 months ago - 3 dependent packages - 22 thousand downloads total - 4 stars on GitHub - 2 maintainers
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
6 versions - Latest release: 8 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
chihaya 1.2.0
Save Delayed Operations to a HDF5 File
3 versions - Latest release: 6 months ago - 1 dependent package - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
beachmat 2.20.0
Compiling Bioconductor to Handle Each Matrix Type
4 versions - Latest release: 15 days ago - 15 dependent packages - 928 thousand downloads total - 4 stars on GitHub - 1 maintainer
matter 2.6.1
Scientific computing for out-of-memory signals and images
5 versions - Latest release: 11 days ago - 2 dependent packages - 19 thousand downloads total - 52 stars on GitHub - 1 maintainer
schex 1.16.1
Hexbin plots for single cell omics data
4 versions - Latest release: 4 months ago - 3 dependent packages - 13.8 thousand downloads total - 71 stars on GitHub - 1 maintainer
Basic4Cseq 1.38.0
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
3 versions - Latest release: 6 months ago - 20.6 thousand downloads total - 1 maintainer
RiboDiPA 1.10.0
Differential pattern analysis for Ribo-seq data
3 versions - Latest release: 6 months ago - 3.28 thousand downloads total - 1 maintainer
OmnipathR 3.10.1
OmniPath web service client and more
3 versions - Latest release: 6 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
APAlyzer 1.16.0
A toolkit for APA analysis using RNA-seq data
3 versions - Latest release: 6 months ago - 6.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
plethy 1.40.0 removed
R framework for exploration and analysis of respirometry data
2 versions - Latest release: 6 months ago - 16.1 thousand downloads total - 1 maintainer
NanoMethViz 2.8.1
Visualise methylation data from Oxford Nanopore sequencing
3 versions - Latest release: 6 months ago - 5.55 thousand downloads total - 20 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...
3 versions - Latest release: 6 months ago - 28.3 thousand downloads total - 1 maintainer
TransView 1.46.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
3 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis
3 versions - Latest release: 6 months ago - 1 dependent package - 10.3 thousand downloads total - 1 maintainer
Rtpca 1.12.0
Thermal proximity co-aggregation with R
3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 1 maintainer
Guitar 2.18.0
Guitar
3 versions - Latest release: 6 months ago - 18.4 thousand downloads total - 1 maintainer
NanoStringNCTools 1.10.1
NanoString nCounter Tools
4 versions - Latest release: about 1 month ago - 2 dependent packages - 14.3 thousand downloads total - 1 maintainer
megadepth 1.12.0
megadepth: BigWig and BAM related utilities
3 versions - Latest release: 6 months ago - 2 dependent packages - 6.86 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
gaggle 1.70.0 removed
Broadcast data between R and Gaggle
2 versions - Latest release: 6 months ago - 31.2 thousand downloads total - 1 maintainer
QSutils 1.20.0
Quasispecies Diversity
3 versions - Latest release: 6 months ago - 19.7 thousand downloads total - 1 maintainer
QTLExperiment 1.0.0
S4 classes for QTL summary statistics and metadata
2 versions - Latest release: 7 months ago - 1 dependent package - 840 downloads total - 1 stars on GitHub - 1 maintainer
Scale4C 1.24.0
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
3 versions - Latest release: 6 months ago - 7.48 thousand downloads total - 1 maintainer
MQmetrics 1.10.0
Quality Control of Protemics Data
3 versions - Latest release: 6 months ago - 2.66 thousand downloads total - 1 maintainer
SICtools 1.32.0
Find SNV/Indel differences between two bam files with near relationship
3 versions - Latest release: 6 months ago - 9.24 thousand downloads total - 1 maintainer
svaNUMT 1.8.0
NUMT detection from structural variant calls
3 versions - Latest release: 6 months ago - 2.46 thousand downloads total - 3 stars on GitHub - 1 maintainer
adductomicsR 1.18.0
Processing of adductomic mass spectral datasets
3 versions - Latest release: 6 months ago - 6.85 thousand downloads total - 1 stars on GitHub - 1 maintainer
BSgenomeForge 1.2.3
Forge BSgenome data packages
5 versions - Latest release: about 1 month ago - 1 dependent package - 8.28 thousand downloads total - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool
1 version - Latest release: 23 days ago - 182 downloads total - 100 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data
3 versions - Latest release: 20 days ago - 8 dependent packages - 85.8 thousand downloads total - 287 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
BioNet 1.62.0
Routines for the functional analysis of biological networks
3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
HiCBricks 1.20.0
Framework for Storing and Accessing Hi-C Data Through HDF Files
3 versions - Latest release: 6 months ago - 1 dependent package - 8.09 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data
3 versions - Latest release: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
3 versions - Latest release: 6 months ago - 3 thousand downloads total - 1 maintainer
GEOfastq 1.10.0
Downloads ENA Fastqs With GEO Accessions
3 versions - Latest release: 6 months ago - 3.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
biodbUniprot 1.8.0
biodbUniprot, a library for connecting to the Uniprot Database
3 versions - Latest release: 6 months ago - 2.48 thousand downloads total - 2 stars on GitHub - 1 maintainer
SynExtend 1.14.0
Tools for Working With Synteny Objects
3 versions - Latest release: 6 months ago - 4.41 thousand downloads total - 1 maintainer
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis
3 versions - Latest release: 6 months ago - 5.56 thousand downloads total - 1 maintainer
flowGate 1.2.0
Interactive Cytometry Gating in R
3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 1 maintainer
alabaster.spatial 1.2.0
Save and Load Spatial 'Omics Data to/from File
3 versions - Latest release: 6 months ago - 1 dependent package - 1.85 thousand downloads total - 1 maintainer
FLAMES 1.8.0
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
3 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 7 stars on GitHub - 1 maintainer
svaRetro 1.8.0
Retrotransposed transcript detection from structural variants
3 versions - Latest release: 6 months ago - 2.44 thousand downloads total - 1 stars on GitHub - 1 maintainer
CTdata 1.2.0
Data companion to CTexploreR
3 versions - Latest release: 6 months ago - 1 dependent package - 1.24 thousand downloads total - 1 stars on GitHub - 1 maintainer
IONiseR 2.26.0
Quality Assessment Tools for Oxford Nanopore MinION data
3 versions - Latest release: 6 months ago - 16 thousand downloads total - 1 maintainer
SimFFPE 1.14.0
NGS Read Simulator for FFPE Tissue
3 versions - Latest release: 6 months ago - 4.18 thousand downloads total - 1 maintainer
HelloRanges 1.28.0
Introduce *Ranges to bedtools users
3 versions - Latest release: 6 months ago - 2 dependent packages - 15.8 thousand downloads total - 1 maintainer
bigmelon 1.28.0
Illumina methylation array analysis for large experiments
3 versions - Latest release: 6 months ago - 12.3 thousand downloads total - 1 maintainer
alabaster.ranges 1.2.0
Load and Save Ranges-related Artifacts from File
3 versions - Latest release: 6 months ago - 2 dependent packages - 5.42 thousand downloads total - 1 maintainer
rhdf5client 1.24.0
Access HDF5 content from HDF Scalable Data Service
3 versions - Latest release: 6 months ago - 4 dependent packages - 11.5 thousand downloads total - 1 maintainer
AnnotationHubData 1.32.1
Transform public data resources into Bioconductor Data Structures
4 versions - Latest release: 3 months ago - 4 dependent packages - 35.4 thousand downloads total - 1 maintainer
Risa 1.44.0
Converting experimental metadata from ISA-tab into Bioconductor data structures
3 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 1 maintainer
IWTomics 1.26.0
Interval-Wise Testing for Omics Data
3 versions - Latest release: 6 months ago - 9.28 thousand downloads total - 1 maintainer
basecallQC 1.26.0
Working with Illumina Basecalling and Demultiplexing input and output files
3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 1 maintainer
podkat 1.34.0
Position-Dependent Kernel Association Test
3 versions - Latest release: 6 months ago - 13.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Spaniel 1.16.0
Spatial Transcriptomics Analysis
3 versions - Latest release: 6 months ago - 6.46 thousand downloads total - 1 maintainer
MuData 1.6.0
Serialization for MultiAssayExperiment Objects
3 versions - Latest release: 6 months ago - 2.13 thousand downloads total - 4 stars on GitHub - 1 maintainer
HiCExperiment 1.2.0
Bioconductor class for interacting with Hi-C files in R
3 versions - Latest release: 6 months ago - 2 dependent packages - 2.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
SpatialOmicsOverlay 1.2.1
Spatial Overlay for Omic Data from Nanostring GeoMx Data
3 versions - Latest release: 6 months ago - 1.68 thousand downloads total - 1 maintainer
R4RNA 1.30.0
An R package for RNA visualization and analysis
3 versions - Latest release: 6 months ago - 2 dependent packages - 30 thousand downloads total - 1 maintainer
ExperimentSubset 1.12.0
Manages subsets of data with Bioconductor Experiment objects
3 versions - Latest release: 6 months ago - 3.77 thousand downloads total - 1 maintainer
SCArray 1.10.0
Large-scale single-cell omics data manipulation with GDS files
3 versions - Latest release: 6 months ago - 1 dependent package - 3.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression
3 versions - Latest release: 6 months ago - 22.2 thousand downloads total - 20 stars on GitHub - 2 maintainers
Top 6.4% on bioconductor.org
hpar 1.44.0
Human Protein Atlas in R
3 versions - Latest release: 6 months ago - 3 dependent packages - 51.2 thousand downloads total - 1 maintainer
alabaster.matrix 1.2.0
Load and Save Artifacts from File
3 versions - Latest release: 6 months ago - 2 dependent packages - 5.74 thousand downloads total - 1 maintainer
alabaster.mae 1.2.0
Load and Save MultiAssayExperiments
3 versions - Latest release: 6 months ago - 1 dependent package - 1.88 thousand downloads total - 1 maintainer
alabaster.vcf 1.2.0
Save and Load Variant Data to/from File
3 versions - Latest release: 6 months ago - 1 dependent package - 1.8 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
genbankr 1.30.0 removed
Parsing GenBank files into semantically useful objects
2 versions - Latest release: 6 months ago - 26 thousand downloads total - 1 maintainer
alabaster.schemas 1.2.0
Schemas for the Alabaster Framework
3 versions - Latest release: 6 months ago - 1 dependent package - 6.05 thousand downloads total - 1 maintainer
alabaster.sce 1.2.0
Load and Save SingleCellExperiment from File
3 versions - Latest release: 6 months ago - 2 dependent packages - 3.03 thousand downloads total - 1 maintainer
alabaster.se 1.2.0
Load and Save SummarizedExperiments from File
3 versions - Latest release: 6 months ago - 4 dependent packages - 5.5 thousand downloads total - 1 maintainer
CNVfilteR 1.16.0
Identifies false positives of CNV calling tools by using SNV calls
3 versions - Latest release: 6 months ago - 5.74 thousand downloads total - 3 stars on GitHub - 1 maintainer
MSstatsConvert 1.12.1
Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format
4 versions - Latest release: 2 months ago - 6 dependent packages - 18.6 thousand downloads total - 1 maintainer
GCSscore 1.16.0 removed
GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
2 versions - Latest release: 6 months ago - 4.11 thousand downloads total - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.74.0
CGH Micro-Array NORmalization
3 versions - Latest release: 6 months ago - 30.2 thousand downloads total - 1 maintainer
psygenet2r 1.34.1
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric...
4 versions - Latest release: 4 months ago - 11.5 thousand downloads total - 1 maintainer
Top 7.2% on bioconductor.org
Rcpi 1.38.0
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
3 versions - Latest release: 6 months ago - 1 dependent package - 33.5 thousand downloads total - 1 maintainer
RImmPort 1.30.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data
3 versions - Latest release: 6 months ago - 9.87 thousand downloads total - 2 maintainers
Related Keywords
Software 331 Sequencing 110 Infrastructure 84 ImmunoOncology 72 DataRepresentation 69 GeneExpression 67 Preprocessing 61 QualityControl 61 Visualization 59 RNASeq 56 SingleCell 48 Coverage 43 Alignment 40 Clustering 37 Microarray 36 Genetics 35 Transcriptomics 34 DifferentialExpression 34 Proteomics 33 Normalization 31 bioconductor 30 Annotation 28 r 26 MultipleComparison 25 Transcription 25 MassSpectrometry 24 TwoChannel 21 Metabolomics 20 OneChannel 19 SequenceMatching 19 BiomedicalInformatics 19 ChIPSeq 18 ThirdPartyClient 18 FunctionalGenomics 17 BatchEffect 16 DNAMethylation 15 Epigenetics 15 GeneSetEnrichment 14 Bayesian 14 Regression 14 SNP 14 bioinformatics 14 Pathways 13 SystemsBiology 12 GenomeAnnotation 12 Classification 12 FlowCytometry 12 GUI 12 Network 11 GeneRegulation 11 ProprietaryPlatforms 11 TimeCourse 11 DifferentialMethylation 10 bioconductor-package 10 CopyNumberVariation 10 CellBasedAssays 10 Cheminformatics 9 CellBiology 9 AlternativeSplicing 9 WorkflowStep 9 mRNAMicroarray 9 VariantAnnotation 9 Spatial 9 MethylationArray 8 rstats 8 GO 8 GraphAndNetwork 8 MethylSeq 8 DifferentialSplicing 7 KEGG 7 MicrotitrePlateAssay 7 ExperimentalDesign 7 MultipleSequenceAlignment 7 ReportWriting 7 DNASeq 7 WholeGenome 7 StatisticalMethod 6 ChipOnChip 6 Microbiome 6 r-package 6 genomics 6 HiC 6 rna-seq 5 GeneticVariability 5 Pharmacogenomics 5 CpGIsland 5 PrincipalComponent 5 DimensionReduction 5 ATACSeq 5 ExonArray 5 GenomeAssembly 4 Pharmacogenetics 4 MotifAnnotation 4 PeakDetection 4 DNA3DStructure 4 sequences 4 Metagenomics 4 MultiChannel 4 GenePrediction 4 RiboSeq 3