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bioconductor-biobase
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public |
Biobase: Base functions for Bioconductor
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2024-11-27 |
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r-facets
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public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
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2024-11-15 |
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bioconductor-protgenerics
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public |
Generic infrastructure for Bioconductor mass spectrometry packages
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2024-11-03 |
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r-grbase
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public |
The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details. NOTICE 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.
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2024-10-22 |
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r-grain
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public |
Probability propagation in graphical independence networks, also known as Bayesian networks or probabilistic expert systems.
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2024-10-17 |
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r-diffcorr
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public |
A method for identifying pattern changes between 2 experimental conditions in correlation networks (e.g., gene co-expression networks), which builds on a commonly used association measure, such as Pearson's correlation coefficient. This package includes functions to calculate correlation matrices for high-dimensional dataset and to test differential correlation, which means the changes in the correlation relationship among variables (e.g., genes and metabolites) between 2 experimental conditions.
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2024-09-30 |
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r-wgcna
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public |
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
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2024-09-18 |
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r-sigqc
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public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
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2024-08-19 |
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r-ic10
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public |
Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
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2024-07-19 |
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r-hemdag
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public |
a collection of Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs).
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2024-06-19 |
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r-spp
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public |
Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) <DOI:10.1038/nbt.1508>].
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2024-06-14 |
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bioconductor-ebseq
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public |
An R package for gene and isoform differential expression analysis of RNA-seq data
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2024-06-07 |
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bioconductor-cytoml
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public |
A GatingML Interface for Cross Platform Cytometry Data Sharing
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2024-06-06 |
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bioconductor-flowdensity
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public |
Sequential Flow Cytometry Data Gating
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2024-06-06 |
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bioconductor-garfield
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public |
GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
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2024-06-06 |
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bioconductor-hilbertvis
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public |
Hilbert curve visualization
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2024-06-06 |
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bioconductor-hyperdraw
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public |
Visualizing Hypergaphs
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2024-06-06 |
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bioconductor-netpathminer
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public |
NetPathMiner for Biological Network Construction, Path Mining and Visualization
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2024-06-04 |
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bioconductor-ebimage
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public |
Image processing and analysis toolbox for R
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2024-05-30 |
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bioconductor-dss
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public |
Dispersion shrinkage for sequencing data
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2024-05-30 |
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bioconductor-bnbc
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public |
Bandwise normalization and batch correction of Hi-C data
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2024-05-30 |
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bioconductor-methylpipe
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public |
Base resolution DNA methylation data analysis
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2024-05-30 |
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bioconductor-bcseq
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public |
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
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2024-05-30 |
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bioconductor-deseq2
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public |
Differential gene expression analysis based on the negative binomial distribution
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2024-05-30 |
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bioconductor-cner
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public |
CNE Detection and Visualization
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2024-05-30 |
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bioconductor-diffbind
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public |
Differential Binding Analysis of ChIP-Seq Peak Data
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2024-05-30 |
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bioconductor-tfbstools
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public |
Software Package for Transcription Factor Binding Site (TFBS) Analysis
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2024-05-30 |
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bioconductor-motifmatchr
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public |
Fast Motif Matching in R
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2024-05-30 |
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bioconductor-esatac
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public |
An Easy-to-use Systematic pipeline for ATACseq data analysis
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2024-05-30 |
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bioconductor-descan2
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public |
Differential Enrichment Scan 2
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2024-05-30 |
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bioconductor-edge
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public |
Extraction of Differential Gene Expression
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2024-05-30 |
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bioconductor-gmapr
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public |
An R interface to the GMAP/GSNAP/GSTRUCT suite
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2024-05-30 |
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bioconductor-contibait
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public |
Improves Early Build Genome Assemblies using Strand-Seq Data
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2024-05-30 |
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bioconductor-clusterexperiment
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public |
Compare Clusterings for Single-Cell Sequencing
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2024-05-30 |
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bioconductor-clipper
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public |
Gene Set Analysis Exploiting Pathway Topology
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2024-05-30 |
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bioconductor-chipcomp
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public |
Quantitative comparison of multiple ChIP-seq datasets
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2024-05-30 |
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bioconductor-biovizbase
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public |
Basic graphic utilities for visualization of genomic data.
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2024-05-30 |
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bioconductor-flagme
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public |
Analysis of Metabolomics GC/MS Data
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2024-05-29 |
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bioconductor-diffhic
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public |
Differential Analyis of Hi-C Data
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2024-05-29 |
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bioconductor-genomation
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public |
Summary, annotation and visualization of genomic data
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2024-05-29 |
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bioconductor-mait
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public |
Statistical Analysis of Metabolomic Data
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2024-05-29 |
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bioconductor-gsva
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public |
Gene Set Variation Analysis for Microarray and RNA-Seq Data
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2024-05-29 |
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bioconductor-casper
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public |
Characterization of Alternative Splicing based on Paired-End Reads
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2024-05-29 |
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bioconductor-qpgraph
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public |
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
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2024-05-29 |
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bioconductor-bsseq
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public |
Analyze, manage and store bisulfite sequencing data
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2024-05-29 |
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bioconductor-scran
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public |
Methods for Single-Cell RNA-Seq Data Analysis
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2024-05-29 |
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bioconductor-cntools
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public |
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
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2024-05-29 |
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bioconductor-csaw
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public |
ChIP-Seq Analysis with Windows
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2024-05-28 |
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bioconductor-rbowtie2
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public |
An R Wrapper for Bowtie2 and AdapterRemoval
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2024-05-28 |
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bioconductor-genegeneinter
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public |
Tools for Testing Gene-Gene Interaction at the Gene Level
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2024-05-28 |
