rhdf5 - R Interface to HDF5
This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
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infrastructuredataimportbioconductorhdf5rhdf5curlopensslcpp
17.01 score 74 stars 283 dependents 5.9k scripts 54k downloads
biomaRt - Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<https://www.ensembl.org/info/data/biomart/index.html>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintained by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
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annotationbioconductorbiomartensembl
15.23 score 51 stars 231 dependents 18k scripts 47k downloads
rhdf5 - R Interface to HDF5
This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
Last updated
infrastructuredataimportbioconductorhdf5rhdf5curlopensslcpp
14.43 score 74 stars 283 dependents 5.9k scriptsDESeq2 - Differential gene expression analysis based on the negative binomial distribution
Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
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sequencingrnaseqchipseqgeneexpressiontranscriptionnormalizationdifferentialexpressionbayesianregressionprincipalcomponentclusteringimmunooncologyopenblascpp
14.31 score 479 stars 134 dependents 42k scripts
biomaRt - Interface to BioMart databases (i.e. Ensembl)
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (<https://www.ensembl.org/info/data/biomart/index.html>). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintained by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
Last updated
annotationbioconductorbiomartensembl
12.59 score 51 stars 217 dependents 18k scripts
Rhdf5lib - hdf5 library as an R package
Provides C and C++ hdf5 libraries.
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infrastructurebioconductorhdf5hdf5-library
11.75 score 7 stars 414 dependents 35 scripts 56k downloadsRarr - A Simple and Performant Native R Reader & Writer for Zarr Arrays
The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.
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dataimportbioconductorome-ngffome-zarron-diskout-of-memoryzarrc-blosclibzstd
10.95 score 55 stars 9 dependents 92 scripts 1.1k downloadsRarr - A Simple and Performant Native R Reader & Writer for Zarr Arrays
The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. Its design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specification in R with minimal reliance on an external tools or libraries.
Last updated
dataimportbioconductorome-ngffome-zarron-diskout-of-memoryzarrc-blosclibzstd
10.93 score 55 stars 9 dependents 92 scripts
rhdf5filters - HDF5 Compression Filters
Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.
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infrastructuredataimportcompressionfilter-pluginhdf5
10.62 score 5 stars 284 dependents 12 scripts 51k downloads
vsn - Variance stabilization and calibration for microarray data
The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
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microarrayonechanneltwochannelpreprocessing
10.53 score 59 dependents 1.6k scripts
vsn - Variance stabilization and calibration for microarray data
The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
Last updated
microarrayonechanneltwochannelpreprocessing
10.37 score 59 dependents 5 scripts 11k downloads
Rhdf5lib - hdf5 library as an R package
Provides C and C++ hdf5 libraries.
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infrastructurebioconductorhdf5hdf5-library
10.08 score 7 stars 422 dependents 35 scriptsEBImage - Image processing and analysis toolbox for R
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
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visualizationcpp
9.91 score 53 dependents 2.8k scripts
rhdf5filters - HDF5 Compression Filters
Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seamless integration with rhdf5, however the compiled filters can also be used with external applications.
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infrastructuredataimportcompressionfilter-pluginhdf5
8.91 score 5 stars 284 dependents 12 scriptsDEXSeq - Inference of differential exon usage in RNA-Seq
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
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immunooncologysequencingrnaseqdifferentialexpressionalternativesplicingdifferentialsplicinggeneexpressionvisualization
8.34 score 10 stars 6 dependents 465 scriptsIHW - Independent Hypothesis Weighting
Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.
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immunooncologymultiplecomparisonrnaseqihwpvalue-adjustment
8.22 score 17 stars 2 dependents 470 scriptsarrayQualityMetrics - Quality metrics report for microarray data sets
This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.
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microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor
8.18 score 1 stars 337 scripts 1.3k downloadslemur - Latent Embedding Multivariate Regression
Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.
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transcriptomicsdifferentialexpressionsinglecelldimensionreductionregressionquartoopenblascpp
8.11 score 102 stars 126 scriptsZarrArray - Bring Zarr datasets in R as DelayedArray objects
The ZarrArray package leverages the Rarr package to bring Zarr datasets in R as DelayedArray objects. The main class in the package is the ZarrArray class. A ZarrArray object is an array-like object that represents a Zarr dataset in R. ZarrArray objects are DelayedArray derivatives and therefore support all operations (delayed or block-processed) supported by DelayedArray objects.
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infrastructuredatarepresentationdataimportbioconductor-packagecore-packageu24ca289073
7.48 score 5 stars 8 dependents 13 scriptsarrayQualityMetrics - Quality metrics report for microarray data sets
This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.
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microarrayqualitycontrolonechanneltwochannelreportwritingbioconductor
7.07 score 1 stars 337 scriptslpsymphony - Symphony integer linear programming solver in R
This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.
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infrastructurethirdpartyclientcoinor-symphony
6.71 score 4 dependents 26 scripts 2.3k downloadstilingArray - Transcript mapping with high-density oligonucleotide tiling arrays
The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class 'segmentation' for representing partitionings of a linear series of data; 2. the function 'segment' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function 'confint' for calculating confidence intervals using the strucchange package; 4. the function 'plotAlongChrom' for generating pretty plots; 5. the function 'normalizeByReference' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.
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microarrayonechannelpreprocessingvisualization
5.78 score 2 dependents 9 scripts 757 downloadsremart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs
This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.
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annotationdataimport
4.98 score 7 stars 4 scriptsHilbertVis - Hilbert curve visualization
Functions to visualize long vectors of integer data by means of Hilbert curves
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visualization
4.92 score 2 dependents 23 scripts 690 downloadsDepInfeR - Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.
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softwareregressionpharmacogeneticspharmacogenomicsfunctionalgenomics
4.66 score 2 stars 23 scripts 374 downloadsromeo - Minimal R 'OME-Zarr' Reader
A minimal R package to reading, writing and validating multiscale OME-Zarr images.
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dataimport
4.62 score 7 stars 4 scriptsremart - Reimplementation of the 'biomaRt' Package Using Modern Ensembl APIs
This package aims to offer a drop-in replacement to biomaRt using the same interface but the more modern and better maintained APIs provided by Ensembl. It provides an easy solution for compatibility with minimal changes for existing projects and packages. New projects may prefer to use another approach which is not constrained by the need for backward compatibility with biomaRt.
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annotationdataimport
4.13 score 4 scriptsHiiragi2013 - Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."
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experimentdatamicroarraydataqpcrdatareproducibleresearch
4.00 score 14 scriptssplots - Visualization of high-throughput assays in microtitre plate or slide format
This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.
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visualizationsequencingmicrotitreplateassay
3.08 score 1 dependents 5 scripts 566 downloadsHD2013SGI - Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping
This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.
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experimentdatacancerdatacoloncancerdatamicrotitreplateassaydatacellculturehomo_sapiens_datahighthroughputimagingdata
2.32 score 6 scriptsdavidTiling - Data and analysis scripts for David, Huber et al. yeast tiling array paper
This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.
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experimentdatagenomesaccharomyces_cerevisiae_datamicroarraydatareproducibleresearch
2.26 score 6 scripts