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Package Name Access Summary Updated
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
bioconductor-deseq2 public Differential gene expression analysis based on the negative binomial distribution 2024-12-27
bioconductor-buscorrect public Batch Effects Correction with Unknown Subtypes 2024-12-27
bioconductor-scuttle public Single-Cell RNA-Seq Analysis Utilities 2024-12-27
bioconductor-apeglm public Approximate posterior estimation for GLM coefficients 2024-12-27
bioconductor-mbkmeans public Mini-batch K-means Clustering for Single-Cell RNA-seq 2024-12-27
bioconductor-biocsingular public Singular Value Decomposition for Bioconductor Packages 2024-12-27
bioconductor-monocle public Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq 2024-12-27
bracken public Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. 2024-12-27
bioconductor-ioniser public Quality Assessment Tools for Oxford Nanopore MinION data 2024-12-27
bioconductor-systempiper public systemPipeR: Workflow Environment for Data Analysis and Report Generation 2024-12-26
bioconductor-rsvsim public RSVSim: an R/Bioconductor package for the simulation of structural variations 2024-12-26
bioconductor-dada2 public Accurate, high-resolution sample inference from amplicon sequencing data 2024-12-26
bioconductor-eatonetalchipseq public ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010 2024-12-26
bioconductor-sevenc public Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs 2024-12-26
r-gkmsvm public Imports the 'gkmSVM' v2.0 functionalities into R <http://www.beerlab.org/gkmsvm/> It also uses the 'kernlab' library (separate R package by different authors) for various SVM algorithms. 2024-12-26
bioconductor-wiggleplotr public Make read coverage plots from BigWig files 2024-12-26
bioconductor-plyranges public A fluent interface for manipulating GenomicRanges 2024-12-26
bioconductor-dmchmm public Differentially Methylated CpG using Hidden Markov Model 2024-12-26
bioconductor-chipenrich.data public Companion package to chipenrich 2024-12-26
r-easylift public A convenience package for converting between popular mouse & human builds. 2024-12-26
bioconductor-roar public Identify differential APA usage from RNA-seq alignments 2024-12-26
bioconductor-seqsetvis public Set Based Visualizations for Next-Gen Sequencing Data 2024-12-26
bioconductor-hitc public High Throughput Chromosome Conformation Capture analysis 2024-12-26
bioconductor-consensusseeker public Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges 2024-12-26
bioconductor-rifi public 'rifi' analyses data from rifampicin time series created by microarray or RNAseq 2024-12-26
bioconductor-r3cseq public Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq) 2024-12-26
bioconductor-chromheatmap public Heat map plotting by genome coordinate 2024-12-26
bioconductor-excluster public ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition 2024-12-26
bioconductor-rificomparative public 'rifiComparative' compares the output of rifi from two different conditions. 2024-12-26
bioconductor-pram public Pooling RNA-seq datasets for assembling transcript models 2024-12-26
bioconductor-scanvis public SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions 2024-12-26
bioconductor-hicvenndiagram public Venn Diagram for genomic interaction data 2024-12-26
bioconductor-ideoviz public Plots data (continuous/discrete) along chromosomal ideogram 2024-12-26
bioconductor-tidycoverage public Extract and aggregate genomic coverage over features of interest 2024-12-26
r-immucellaimouse public ImmuCellAI-mouse is a tool to estimate the abundance of 36 immune cells based on gene expression profile from RNA-Seq or microarray data. 2024-12-26
bioconductor-normr public Normalization and difference calling in ChIP-seq data 2024-12-26
bioconductor-hicaggr public Set of 3D genomic interaction analysis tools 2024-12-26
r-sigqc 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. 2024-12-26
bioconductor-dmcfb public Differentially Methylated Cytosines via a Bayesian Functional Approach 2024-12-26
bioconductor-epidecoder public epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation 2024-12-26
bioconductor-motifdb public An Annotated Collection of Protein-DNA Binding Sequence Motifs 2024-12-26
bioconductor-scpipe public Pipeline for single cell multi-omic data pre-processing 2024-12-26
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