Biocview "DataImport"

Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Accelerated similarity searching of small molecules
Access HDF5 content from h5serv
Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
Access to the InSilico Database
A compilation of ENCODE metadata
A compilation of ENCODE metadata
A compilation of ENCODE metadata
A compilation of ENCODE metadata
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
A compilation of metadata from NCBI SRA and tools
Add resources to ExperimentHub
Add resources to ExperimentHub
Add resources to ExperimentHub
Affymetrix File Parsing SDK
Affymetrix File Parsing SDK
Affymetrix File Parsing SDK
A generic R plugin dispatcher for BASE
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of Agilent Microarray Data [draft]
Analysis of Brain Imaging Data
Analysis of Illumina microarray data [A DRAFT - TRUE]
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analytical Tools for MassArray Data
Analytical Tools for MassArray Data
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
An interface package for the BIOM file format
An interface package for the BIOM file format
An interface package for the BIOM file format
An interface package for the BIOM file format
An mzIdentML parser for R
An mzIdentML parser for R
An mzIdentML parser for R
Annotation and analysis of biological dynamical systems using flow cytometry
Annotation and analysis of biological dynamical systems using flow cytometry
Annotation and analysis of biological dynamical systems using flow cytometry
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database
Annotation of Genetic Variants
Annotation of Genetic Variants
Annotation of Genetic Variants
An R Object-oriented Microarray Analysis package
An R package for RNA visualization and analysis
An R package for RNA visualization and analysis
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
A package for importing and analyzing data from Roche's Genome Sequencer System
A package for importing and analyzing data from Roche's Genome Sequencer System
A probe-level data file format used by aroma.affymetrix [DEPRECATED]
A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
A Thin Wrapper around the ImmuneSpace Database
A Thin Wrapper around the ImmuneSpace Database
A Thin Wrapper around the ImmuneSpace Database
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
Augmented functionality for analysis of epigenomic variance
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
A work flow for analysis and normalization of pre-processing RT-qPCR data
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Classes and Functions for Phylogenetic Tree Input and Output
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions and Classes for Mass Spectrometry and Proteomics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Bioconductor Algorithms for Big Data
Broadcast data between R and Gaggle
Broadcast data between R and Gaggle
CDF Environment Maker
CDF Environment Maker
Cell OrderiNg by FluorEScence Signal
Cell OrderiNg by FluorEScence Signal
CGH Micro-Array NORmalization
CGH Micro-Array NORmalization
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
Cheminformatics Toolkit for R
ChIPanalyser: Predicting Transcription Factor Binding Sites
chipseq: A package for analyzing chipseq data
chipseq: A package for analyzing chipseq data
ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures
Classes and functions for Array Comparative Genomic Hybridization data.
Classes and functions for Array Comparative Genomic Hybridization data.
Client to access AnnotationHub resources
Client to access AnnotationHub resources
Client to access ExperimentHub resources
Client to access ExperimentHub resources
Client to access ExperimentHub resources
Cluster and Tree Conversion.
Cluster and Tree Conversion.
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
CNE Detection and Visualization
CNE Detection and Visualization
CNE Detection and Visualization
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Compiling Bioconductor to Handle Each Matrix Type
Compute coverage matrices from recount quickly using bwtool
Convenience package for solving some liftover challenges
Convenience package for solving some liftover challenges
Converting experimental metadata from ISA-tab into Bioconductor data structures
Converting experimental metadata from ISA-tab into Bioconductor data structures
Converting experimental metadata from ISA-tab into Bioconductor data structures
Convert the GatingSet from Boost serialization to protocol buffer format
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
Cross-target analysis of small molecule bioactivity
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
DeepBlueR
DeepBlueR
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Detection of subclonal SNVs in deep sequencing data.
Distributed computing by file or by range
Distributed computing by file or by range
Distributed computing by file or by range
Easy Handling of and Access to Files Organized in Structured Directories
Easy Handling of and Access to Files Organized in Structured Directories
Efficient algorithms for DNA methylation
Efficient compression and analysis of Hi-C Data
Efficient manipulation of biological strings
Enabling stream processing of large files
Enabling stream processing of large files
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extract read count signals from bam files
Extract read count signals from bam files
Extract read count signals from bam files
Fast full-text and DNA search in NCBI RefSeq, UniProt-KB and genome sequence
FASTQ input and manipulation
FASTQ input and manipulation
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Find SNV/Indel differences between two bam files with near relationship
Find SNV/Indel differences between two bam files with near relationship
Fitting cell population growth models
Fitting cell population growth models
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
GatingML interface for openCyto
GatingML interface for openCyto
GatingML interface for openCyto
GEM: fast association study for the interplay of Gene, Environment and Methylation
Gene Expression Atlas query and gene set enrichment package.
Gene Expression Atlas query and gene set enrichment package.
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
GeneRegionScan
GeneRegionScan
Generic and Biological Sequences
Generic and Biological Sequences
Gene transfer format files for common ChIP-seq model organisms
Get data from NCBI Gene Expression Omnibus (GEO)
Get data from NCBI Gene Expression Omnibus (GEO)
Get data from NCBI Gene Expression Omnibus (GEO)
Get data from NCBI Gene Expression Omnibus (GEO)
GMQL function
gQTLBase: infrastructure for eQTL, mQTL and similar studies
gQTLBase: infrastructure for eQTL, mQTL and similar studies
GUI for limma package with Affymetrix microarrays
GUI for limma package with Affymetrix microarrays
GUI for limma package with two color microarrays
GUI for limma package with two color microarrays
Guitar
Guitar
GWAS trait-associated SNP enrichment analyses in genomic intervals
GWAS trait-associated SNP enrichment analyses in genomic intervals
HDF5 interface to R
HDF5 interface to R
Hierarchical Gating Pipeline for flow cytometry data
Hierarchical Gating Pipeline for flow cytometry data
High throughput prioritized acquisition and processing of tandem mass spectra
High-Throughput Sequence Analysis using the Aroma Framework
htslib high-throughput sequencing library as an R package
HTSlib high-throughput sequencing library as an R package
HTSlib high-throughput sequencing library as an R package
Human ChIP-seq peaks data from ENCODE and ROADMAP Epigenomics
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Identifying differential DNA loops from chromatin topology data
Illumina methylation array analysis for large experiments
Illumina methylation array analysis for large experiments
Illumina methylation array analysis for large experiments
Import and summarize transcript-level estimates for gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import, modify, and export motif files with R
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Import, process and analysis of Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) imaging data
Infrastructure for representing and interacting with the gated cytometry
Infrastructure for representing and interacting with the gated cytometry
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs
Interaction Based Homogeneity for Evaluating Gene Lists
Interaction Based Homogeneity for Evaluating Gene Lists
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Linear Models for Microarray Data
Linear Models for Microarray Data
Linear Models for Microarray Data
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
Manage Files Across Sessions
Manage Files Across Sessions
Manage Files Across Sessions
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Manipulating and exploring protein and proteomics data
Manipulation of Codelink microarray data
Manipulation of Codelink microarray data
Methods for accessing online The Cancer Genome Atlas (TCGA) data
Methods for accessing online The Cancer Genome Atlas (TCGA) data
Methods for Continuous Flow Cytometry
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for reading CNAG files
Methods for reading CNAG files
Methods for reading dChip files
Methods for Reading dChip Files
Methods for Reading dChip Files
Microarray Analysis of Differential Expression
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Mismatch Tolerant Maximum Common Substructure Searching
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functions
Multiple Sequence Alignment with MUSCLE
Multiple Sequence Alignment with MUSCLE
NDEx R client library
NIH / NCI Genomic Data Commons Access
NIH / NCI Genomic Data Commons Access
NIH / NCI Genomic Data Commons Access
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and reporting of Illumina SNP bead arrays
Normalization and reporting of Illumina SNP bead arrays
OnASSIs Ontology Annotation and Semantic SImilarity software
OnASSIs Ontology Annotation and Semantic SImilarity software
Operations on genomic intervals
Operations on genomic intervals
Optimal Gene Extensions From Histone Modification ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Package for CTDbase data query, visualization and downstream analysis.
Parallel queries distributed by file or by range
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)
parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
Parsing GenBank files into semantically useful objects
Parsing GenBank files into semantically useful objects
Parsing Illumina Microarray Output Files
Parsing Illumina Microarray Output Files
Parsing Illumina Microarray Output Files
Perform Methylation Analysis on Next Generation Sequencing Data
Perform Methylation Analysis on Next Generation Sequencing Data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Position-Dependent Kernel Association Test
Position-Dependent Kernel Association Test
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays.
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Proteomics Standard Initiative Common QUery InterfaCe
Proteomics Standard Initiative Common QUery InterfaCe
Provides access to pathogen annotation resources available on EuPathDB databases
Provides access to pathogen annotation resources available on EuPathDB databases
Provides structure and functions for the analysis of OTU data
Provides structure and functions for the analysis of OTU data
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders
QA/QC of a gVCF or VCF file
QA/QC of a gVCF or VCF file
Quality Assessment Tools for Oxford Nanopore MinION data
Quality Assessment Tools for Oxford Nanopore MinION data
Quality Control Tool for High-Throughput Sequencing Data
Quality Control Tool for High-Throughput Sequencing Data
Quality Control Tool for High-Throughput Sequencing Data
Quantitative comparison of multiple ChIP-seq datasets
Quantitative comparison of multiple ChIP-seq datasets
query gene expression data and plots from BrainStars (B*)
query gene expression data and plots from BrainStars (B*)
Quick Read Quality Control
Quick Read Quality Control
Quick Read Quality Control
R Client for GA4GH API
R Client for Google Genomics API
R Client for Google Genomics API
R Client for Google Genomics API
R Client for Seven Bridges Genomics API (v1)
R Client for Seven Bridges Platform API
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read qPCR data
Read qPCR data
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
R framework for exploration and analysis of respirometry data
R framework for exploration and analysis of respirometry data
R framework for exploration and analysis of respirometry data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
RImmPort: Enabling Ready-for-analysis Immunology Research Data
R interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R interface to a subset of OpenBabel functionalities
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to CoreArray Genomic Data Structure (GDS) Files
R Interface to CoreArray Genomic Data Structure (GDS) Files
R interface to genome browsers and their annotation tracks
R interface to genome browsers and their annotation tracks
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
R Interface to the ProteomeXchange Repository
R Investigation of ChIP-chip Oligoarrays
R Investigation of ChIP-chip Oligoarrays
RNA-Seq Utilities
RNA-Seq Utilities
RnBeads
RnBeads
Routines for the functional analysis of biological networks
Routines for the functional analysis of biological networks
Routines that don't belong to the core flow packages yet.
R package for handling genomic interaction data
R package for handling genomic interaction data
R package for handling genomic interaction data
R package implementing the Cytoscape Exchange (CX) format
R SDK for BaseSpace RESTful API
R SDK for BaseSpace RESTful API
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
rSFFreader reads in sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Segvis: A package for visualization of high throughout sequencing data along genomic segments
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
Similarity measures for chemical compounds
Similarity measures for chemical compounds
Simple tiling array analysis of Affymetrix ChIP-chip data
Simple tiling array analysis of Affymetrix ChIP-chip data
Single-cell analysis toolkit for gene expression data in R
Single-cell analysis toolkit for gene expression data in R
Single-cell analysis toolkit for gene expression data in R
Single-Cell RNA-Seq Utilities
Statistical analysis of Solexa sequencing data
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
String objects representing biological sequences, and matching algorithms
String objects representing biological sequences, and matching algorithms
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Test Single Package Builder
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
Tools for analysing methylation patterns at genomic tuples
Tools for curating, analyzing, and manipulating biological sequences
Tools for curating, analyzing, and manipulating biological sequences
Tools for HELP data analysis
Tools for HELP data analysis
Tools for masking out problematic Affymetrix probes using VCF files and the oligo package
Tools for parsing Affymetrix data files
Tools for parsing Affymetrix data files
Tools for the Differential Analysis of Proteins Abundance with R
Tools for the Differential Analysis of Proteins Abundance with R
Transcriptome-guided quality assessment of methylated RNA immunoprecipitation sequencing data
Transform public data resources into Bioconductor Data Structures
Transform public data resources into Bioconductor Data Structures
Transform public data resources into Bioconductor Data Structures
Transform public proteomics data resources into Bioconductor Data Structures
Transform public proteomics data resources into Bioconductor Data Structures
Transform public proteomics data resources into Bioconductor Data Structures
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
Working with Illumina Basecalling and Demultiplexing input and output files
You Only Lookup One (small part of an otherwise large matrix)