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bioconductor-survcomp
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public |
Performance Assessment and Comparison for Survival Analysis
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2025-08-12 |
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bioconductor-hmmcopy
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public |
Copy number prediction with correction for GC and mappability bias for HTS data
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2025-07-21 |
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bioconductor-lpsymphony
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public |
Symphony integer linear programming solver in R
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2025-07-17 |
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bioconductor-rbowtie2
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public |
An R Wrapper for Bowtie2 and AdapterRemoval
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2025-07-17 |
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r-rphast
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public |
Provides an R interface to the 'PHAST'(<http://compgen.cshl.edu/phast/>) software (Phylogenetic Analysis with Space/Time Models). It can be used for many types of analysis in comparative and evolutionary genomics, such as estimating models of evolution from sequence data, scoring alignments for conservation or acceleration, and predicting elements based on conservation or custom phylogenetic hidden Markov models. It can also perform many basic operations on multiple sequence alignments and phylogenetic trees.
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2025-07-08 |
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r-exomedepth
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public |
Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.
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2025-06-30 |
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bioconductor-dmrcate
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public |
Methylation array and sequencing spatial analysis methods
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2025-06-29 |
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bioconductor-missmethyl
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public |
Analysing Illumina HumanMethylation BeadChip Data
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2025-06-27 |
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bioconductor-geometadb
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public |
A compilation of metadata from NCBI GEO
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2025-06-21 |
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r-isogene
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public |
Offers framework for testing for monotonic relationship between gene expression and doses in a microarray experiment. Several testing procedures including the global likelihood-ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus (1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007) are used to test for the monotonic trend in gene expression with respect to doses. BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2004) FDR controlling procedures are applied to adjust the raw p-values obtained from the permutations.
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2025-06-18 |
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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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2025-06-12 |
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r-htssip
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public |
Functions for analyzing high throughput sequencing stable isotope probing (HTS-SIP) data. Analyses include high resolution stable isotope probing (HR-SIP), multi-window high resolution stable isotope probing (MW-HR-SIP), and quantitative stable isotope probing (q-SIP).
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2025-06-11 |
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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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2025-06-08 |
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bioconductor-dirichletmultinomial
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public |
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
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2025-06-02 |
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bioconductor-decipher
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public |
Tools for curating, analyzing, and manipulating biological sequences
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2025-05-29 |
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bioconductor-pics
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public |
Probabilistic inference of ChIP-seq
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2025-04-30 |
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bioconductor-switchbox
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public |
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
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2025-04-30 |
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bioconductor-adsplit
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public |
Annotation-Driven Clustering
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2025-04-30 |
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bioconductor-gcrma
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public |
Background Adjustment Using Sequence Information
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2025-04-30 |
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bioconductor-beadarray
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public |
Quality assessment and low-level analysis for Illumina BeadArray data
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2025-04-30 |
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bioconductor-ternarynet
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public |
Ternary Network Estimation
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2025-04-30 |
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bioconductor-makecdfenv
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public |
CDF Environment Maker
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2025-04-30 |
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bioconductor-microrna
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public |
Data and functions for dealing with microRNAs
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2025-04-30 |
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bioconductor-netpathminer
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public |
NetPathMiner for Biological Network Construction, Path Mining and Visualization
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2025-04-30 |
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bioconductor-messina
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public |
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
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2025-04-30 |
