Group: Renjin Bioconductor

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1. AnnotationDbi368 usages

org.renjin.bioconductor » AnnotationDbiArtistic

Provides user interface and database connection code for annotation data packages using SQLite data storage.
Last Release on Apr 28, 2022

2. Biobase360 usages

org.renjin.bioconductor » BiobaseArtistic

Functions that are needed by many other packages or which replace R functions.
Last Release on Feb 14, 2021

3. BiocGenerics216 usages

org.renjin.bioconductor » BiocGenericsArtistic

S4 generic functions needed by many Bioconductor packages.
Last Release on Apr 29, 2022

4. LIMMA129 usages

org.renjin.bioconductor » limma

Data analysis, linear models and differential expression for microarray data.
Last Release on Feb 16, 2021

5. IRanges112 usages

org.renjin.bioconductor » IRangesArtistic

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Last Release on Apr 29, 2022

6. GenomicRanges104 usages

org.renjin.bioconductor » GenomicRangesArtistic

The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the ...
Last Release on Apr 28, 2022

7. S4Vectors96 usages

org.renjin.bioconductor » S4VectorsArtistic

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure ...
Last Release on Feb 13, 2021

8. Graph81 usages

org.renjin.bioconductor » graphArtistic

A package that implements some simple graph handling capabilities.
Last Release on Apr 30, 2022

9. Affy79 usages

org.renjin.bioconductor » affyLGPL

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
Last Release on Apr 28, 2022

10. SummarizedExperiment76 usages

org.renjin.bioconductor » SummarizedExperimentArtistic

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.
Last Release on Apr 29, 2022

11. Biostrings69 usages

org.renjin.bioconductor » BiostringsArtistic

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.
Last Release on Apr 28, 2022

12. Annotate59 usages

org.renjin.bioconductor » annotateArtistic

Using R enviroments for annotation.
Last Release on Apr 29, 2022

13. EdgeR55 usages

org.renjin.bioconductor » edgeR

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.
Last Release on Feb 16, 2021

14. BiocStyle51 usages

org.renjin.bioconductor » BiocStyleArtistic

Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.
Last Release on Feb 13, 2021

15. Genefilter48 usages

org.renjin.bioconductor » genefilterArtistic

Some basic functions for filtering genes
Last Release on Apr 28, 2022

16. BiocParallel40 usages

org.renjin.bioconductor » BiocParallelGPL

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.
Last Release on Apr 28, 2022

17. Rsamtools39 usages

org.renjin.bioconductor » RsamtoolsArtistic

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Last Release on Apr 28, 2022

18. Multtest39 usages

org.renjin.bioconductor » multtestLGPL

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety ...
Last Release on Apr 28, 2022

19. Hs EG DB39 usages

org.renjin.bioconductor »

Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.
Last Release on Apr 28, 2022

20. GO DB38 usages

org.renjin.bioconductor » GO.dbArtistic

A set of annotation maps describing the entire Gene Ontology assembled using data from GO
Last Release on Apr 30, 2022