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 Jul 24, 2024
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
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
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
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
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
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 » org.Hs.eg.dbArtistic
Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.
Last Release on Apr 28, 2022