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bioconductor-cfassay
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public |
Statistical analysis for the Colony Formation Assay
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2024-12-14 |
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bioconductor-indeed
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public |
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
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2024-12-14 |
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bioconductor-vbmp
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public |
Variational Bayesian Multinomial Probit Regression
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2024-12-14 |
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bioconductor-mdp
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public |
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
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2024-12-14 |
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bioconductor-m3c
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public |
Monte Carlo Reference-based Consensus Clustering
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2024-12-14 |
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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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2024-12-14 |
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bioconductor-lpsymphony
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public |
Symphony integer linear programming solver in R
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2024-12-14 |
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bioconductor-survcomp
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public |
Performance Assessment and Comparison for Survival Analysis
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2024-12-14 |
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bioconductor-snm
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public |
Supervised Normalization of Microarrays
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2024-12-14 |
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bioconductor-gem
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public |
GEM: fast association study for the interplay of Gene, Environment and Methylation
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2024-12-14 |
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bioconductor-mpfe
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public |
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
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2024-12-14 |
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bioconductor-asgsca
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public |
Association Studies for multiple SNPs and multiple traits using Generalized Structured Equation Models
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2024-12-14 |
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bioconductor-demand
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public |
DeMAND
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2024-12-14 |
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bioconductor-igc
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public |
An integrated analysis package of Gene expression and Copy number alteration
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2024-12-14 |
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bioconductor-clusterjudge
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public |
Judging Quality of Clustering Methods using Mutual Information
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2024-12-14 |
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bioconductor-semisup
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public |
Semi-Supervised Mixture Model
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2024-12-14 |
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bioconductor-ntw
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public |
Predict gene network using an Ordinary Differential Equation (ODE) based method
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2024-12-14 |
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bioconductor-synergyfinder
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public |
Calculate and Visualize Synergy Scores for Drug Combinations
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2024-12-14 |
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bioconductor-biocgenerics
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public |
S4 generic functions used in Bioconductor
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2024-12-14 |
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bioconductor-consensus
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public |
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
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2024-12-14 |
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bioconductor-rnaseqpower
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public |
Sample size for RNAseq studies
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2024-12-14 |
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bioconductor-gpls
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public |
Classification using generalized partial least squares
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2024-12-14 |
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bioconductor-metahdep
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public |
Hierarchical Dependence in Meta-Analysis
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2024-12-14 |
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bioconductor-mantelcorr
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public |
Compute Mantel Cluster Correlations
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2024-12-14 |
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bioconductor-geneticsped
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public |
Pedigree and genetic relationship functions
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2024-12-14 |
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bioconductor-sizepower
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public |
Sample Size and Power Calculation in Micorarray Studies
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2024-12-14 |
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bioconductor-empiricalbrownsmethod
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public |
Uses Brown's method to combine p-values from dependent tests
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2024-12-14 |
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bioconductor-macorrplot
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public |
Visualize artificial correlation in microarray data
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2024-12-14 |
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bioconductor-treeio
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public |
Base Classes and Functions for Phylogenetic Tree Input and Output
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2024-12-14 |
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bioconductor-agilp
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public |
Agilent expression array processing package
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2024-12-14 |
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bioconductor-specl
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public |
specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
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2024-12-14 |
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bioconductor-rimmport
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public |
RImmPort: Enabling Ready-for-analysis Immunology Research Data
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2024-12-14 |
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bioconductor-multimed
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public |
Testing multiple biological mediators simultaneously
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2024-12-14 |
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bioconductor-clustcomp
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public |
Clustering Comparison Package
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2024-12-14 |
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bioconductor-stringdb
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public |
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
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2024-12-14 |
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bioconductor-pmm
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public |
Parallel Mixed Model
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2024-12-14 |
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bioconductor-scfeaturefilter
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public |
A correlation-based method for quality filtering of single-cell RNAseq data
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2024-12-14 |
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bioconductor-asafe
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public |
Ancestry Specific Allele Frequency Estimation
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2024-12-14 |
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bioconductor-mbttest
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public |
Multiple Beta t-Tests
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2024-12-14 |
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bioconductor-qvalue
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public |
Q-value estimation for false discovery rate control
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2024-12-14 |
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bioconductor-chicago
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public |
CHiCAGO: Capture Hi-C Analysis of Genomic Organization
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2024-12-14 |
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bioconductor-mapscape
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public |
mapscape
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2024-12-14 |
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bioconductor-targetscore
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public |
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
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2024-12-14 |
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r-phyext2
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public |
Based on (but not identical to) the no-longer-maintained package 'phyext', provides enhancements to 'phylobase' classes, specifically for use by package 'SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in 'SigTree'); also provides support for a few other extra features.
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2024-12-14 |
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r-ggbiplot
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public |
A biplot based on ggplot2
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2024-12-14 |
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r-tcr
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public |
Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.
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2024-12-14 |
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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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2024-12-14 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
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2024-12-12 |
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r-gwpcr
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public |
Implements the necessary distributions and parameter estimation procedures for a model of amplification and high-troughput sequencing. The model is based on a mechanistic model of PCR amplification as a Galton-Watson branching process, and on Poissonan sampling to model high-throughput sequencing.
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2024-12-11 |
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bioconductor-mpra
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public |
Analyze massively parallel reporter assays
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2024-12-11 |
