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Package Name Access Summary Updated
bioconductor-rtnsurvival public Survival analysis using transcriptional networks inferred by the RTN package 2024-12-27
phabox public Virus identification and analysis tool set 2024-12-27
bioconductor-coseq public Co-Expression Analysis of Sequencing Data 2024-12-27
bioconductor-isomirs public Analyze isomiRs and miRNAs from small RNA-seq 2024-12-27
r-xcell public Estimate immune cell proportions from gene expression data 2024-12-27
bioconductor-slingshot public Tools for ordering single-cell sequencing 2024-12-27
bioconductor-oppar public Outlier profile and pathway analysis in R 2024-12-27
bioconductor-tscan public Tools for Single-Cell Analysis 2024-12-27
bioconductor-cbea public Competitive Balances for Taxonomic Enrichment Analysis in R 2024-12-27
bioconductor-gsva public Gene Set Variation Analysis for Microarray and RNA-Seq Data 2024-12-27
bioconductor-plsdabatch public PLSDA-batch 2024-12-27
bioconductor-miasim public Microbiome Data Simulation 2024-12-27
bioconductor-treeclimbr public An algorithm to find optimal signal levels in a tree 2024-12-27
bioconductor-microstasis public Microbiota STability ASsessment via Iterative cluStering 2024-12-27
bioconductor-gsean public Gene Set Enrichment Analysis with Networks 2024-12-27
bioconductor-celaref public Single-cell RNAseq cell cluster labelling by reference 2024-12-27
bioconductor-powsc public Simulation, power evaluation, and sample size recommendation for single cell RNA-seq 2024-12-27
bioconductor-opossom public Comprehensive analysis of transcriptome data 2024-12-27
r-scopfunctions public An R package of functions for single cell -omics analysis. 2024-12-27
r-dwls public Deconvolution of bulk mRNA data using single-cell RNAseq to provide cell type specific signatures 2024-12-27
bioconductor-iseehex public iSEE extension for summarising data points in hexagonal bins 2024-12-27
bioconductor-iseepathways public iSEE extension for panels related to pathway analysis 2024-12-27
bioconductor-cnordt public Add-on to CellNOptR: Discretized time treatments 2024-12-27
bioconductor-iseede public iSEE extension for panels related to differential expression analysis 2024-12-27
bioconductor-cnorfuzzy public Addon to CellNOptR: Fuzzy Logic 2024-12-27
bioconductor-spectraltad public SpectralTAD: Hierarchical TAD detection using spectral clustering 2024-12-27
bioconductor-cnorode public ODE add-on to CellNOptR 2024-12-27
bioconductor-multihiccompare public Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available 2024-12-27
bioconductor-mnem public Mixture Nested Effects Models 2024-12-27
bioconductor-netresponse public Functional Network Analysis 2024-12-27
bioconductor-tadcompare public TADCompare: Identification and characterization of differential TADs 2024-12-27
bioconductor-cellnoptr public Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data 2024-12-27
bioconductor-hicool public HiCool 2024-12-27
bioconductor-oncosimulr public Forward Genetic Simulation of Cancer Progression with Epistasis 2024-12-27
bioconductor-hicontacts public Analysing cool files in R with HiContacts 2024-12-27
bioconductor-segmentseq public Methods for identifying small RNA loci from high-throughput sequencing data 2024-12-27
bioconductor-streamer public Enabling stream processing of large files 2024-12-27
bioconductor-chipsim public Simulation of ChIP-seq experiments 2024-12-27
bioconductor-rbioinf public RBioinf 2024-12-27
r-motifbinner public MotifBinner processes high-throughput sequencing data of an RNA virus population. 2024-12-27
bioconductor-rtreemix public Rtreemix: Mutagenetic trees mixture models. 2024-12-27
bioconductor-nucler public Nucleosome positioning package for R 2024-12-27
bioconductor-basecallqc public Working with Illumina Basecalling and Demultiplexing input and output files 2024-12-27
r-rspectral public Implements the network clustering algorithm described in Newman (2006) <doi:10.1103/PhysRevE.74.036104>. The complete iterative algorithm comprises of two steps. In the first step, the network is expressed in terms of its leading eigenvalue and eigenvector and recursively partition into two communities. Partitioning occurs if the maximum positive eigenvalue is greater than the tolerance (10e-5) for the current partition, and if it results in a positive contribution to the Modularity. Given an initial separation using the leading eigen step, 'rSpectral' then continues to maximise for the change in Modularity using a fine-tuning step - or variate thereof. The first stage here is to find the node which, when moved from one community to another, gives the maximum change in Modularity. This node’s community is then fixed and we repeat the process until all nodes have been moved. The whole process is repeated from this new state until the change in the Modularity, between the new and old state, is less than the predefined tolerance. A slight variant of the fine-tuning step, which can improve speed of the calculation, is also provided. Instead of moving each node into each community in turn, we only consider moves of neighbouring nodes, found in different communities, to the community of the current node of interest. The two steps process is repeatedly applied to each new community found, subdivided each community into two new communities, until we are unable to find any division that results in a positive change in Modularity. 2024-12-27
bioconductor-otubase public Provides structure and functions for the analysis of OTU data 2024-12-27
r-wgcna 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. 2024-12-27
bioconductor-gosemsim public GO-terms Semantic Similarity Measures 2024-12-27
bioconductor-batchelor public Single-Cell Batch Correction Methods 2024-12-27
bioconductor-interactionset public Base Classes for Storing Genomic Interaction Data 2024-12-27
bioconductor-scran public Methods for Single-Cell RNA-Seq Data Analysis 2024-12-27
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