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bioconductor-gosummaries
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public |
Word cloud summaries of GO enrichment analysis
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2023-12-04 |
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bioconductor-lpeadj
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public |
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
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2023-12-04 |
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bioconductor-moda
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public |
MODA: MOdule Differential Analysis for weighted gene co-expression network
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2023-12-04 |
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bioconductor-ebseqhmm
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public |
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
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2023-12-04 |
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bioconductor-correp
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public |
Multivariate Correlation Estimator and Statistical Inference Procedures.
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2023-12-04 |
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bioconductor-smap
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public |
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
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2023-12-03 |
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bioconductor-squadd
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public |
Add-on of the SQUAD Software
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2023-12-03 |
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bioconductor-rdgidb
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public |
R Wrapper for DGIdb
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2023-12-03 |
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bioconductor-suprahex
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public |
supraHex: a supra-hexagonal map for analysing tabular omics data
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2023-12-03 |
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bioconductor-bhc
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public |
Bayesian Hierarchical Clustering
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2023-12-03 |
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bioconductor-typeinfo
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public |
Optional Type Specification Prototype
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2023-12-03 |
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bioconductor-nanostringqcpro
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public |
Quality metrics and data processing methods for NanoString mRNA gene expression data
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2023-07-19 |
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bioconductor-chromswitch
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public |
An R package to detect chromatin state switches from epigenomic data
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2023-07-18 |
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bioconductor-cancersubtypes
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public |
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
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2023-07-18 |
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bioconductor-eegc
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public |
Engineering Evaluation by Gene Categorization (eegc)
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2023-07-18 |
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bioconductor-kissde
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public |
Retrieves Condition-Specific Variants in RNA-Seq Data
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2023-07-18 |
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bioconductor-crisprseekplus
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public |
crisprseekplus
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2023-07-18 |
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r-xgr
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public |
The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
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2023-07-17 |
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r-sigtree
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public |
Provides tools to identify and visualize branches in a phylogenetic tree that are significantly responsive to some intervention, taking as primary inputs a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip (OTU) labels and p-values.
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2023-07-17 |
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bioconductor-chic
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public |
Quality Control Pipeline for ChIP-Seq Data
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2023-07-17 |
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r-metalonda
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public |
Identify time intervals of differentially abundant metagenomics features in longitudinal studies.
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2023-07-17 |
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bioconductor-refplus
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public |
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
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2023-07-17 |
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bioconductor-metab
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public |
Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.
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2023-07-17 |
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bioconductor-dmrforpairs
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public |
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
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2023-07-16 |
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bioconductor-foldgo
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public |
Package for Fold-specific GO Terms Recognition
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2023-07-16 |
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bioconductor-sispa
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public |
SISPA: Method for Sample Integrated Set Profile Analysis
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2023-07-15 |
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bioconductor-metagene
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public |
A package to produce metagene plots
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2023-07-15 |
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r-dnet
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public |
The focus of the dnet by Fang and Gough (2014) <doi:10.1186/s13073-014-0064-8> is to make sense of omics data (such as gene expression and mutations) from different angles including: integration with molecular networks, enrichments using ontologies, and relevance to gene evolutionary ages. Integration is achieved to identify a gene subnetwork from the whole gene network whose nodes/genes are labelled with informative data (such as the significant levels of differential expression or survival risks). To help make sense of identified gene networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including: human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for calculating semantic similarity between ontology terms (and between genes) and for calculating network affinity based on random walk; both can be done via high-performance parallel computing.
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2023-07-15 |
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bioconductor-genbankr
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public |
Parsing GenBank files into semantically useful objects
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2023-07-14 |
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bioconductor-compartmap
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public |
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq
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2023-07-14 |
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bioconductor-alpine
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public |
alpine
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2023-07-14 |
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bioconductor-alpinedata
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public |
Data for the alpine package vignette
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2023-07-13 |
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r-fgwas
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public |
GWAS tools for longitudinal genetic traits based on fGWAS statistical model.
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2023-07-13 |
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bioconductor-bgmix
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public |
Bayesian models for differential gene expression
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2023-07-12 |
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r-samr
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public |
Significance Analysis of Microarrays
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2023-07-12 |
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bioconductor-fcbf
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public |
Fast Correlation Based Filter for Feature Selection
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2023-07-11 |
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bioconductor-multiomicsviz
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public |
Plot the effect of one omics data on other omics data along the chromosome
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2023-07-11 |
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bioconductor-mirmine
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public |
Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperiment
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2023-07-11 |
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bioconductor-neighbornet
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public |
Neighbor_net analysis
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2023-07-11 |
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bioconductor-sscore
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public |
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
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2023-07-11 |
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bioconductor-farms
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public |
FARMS - Factor Analysis for Robust Microarray Summarization
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2023-07-10 |
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bioconductor-logitt
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public |
logit-t Package
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2023-07-10 |
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bioconductor-tweedeseqcountdata
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public |
RNA-seq count data employed in the vignette of the tweeDEseq package
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2023-07-10 |
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bioconductor-stroma4
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public |
Assign Properties to TNBC Patients
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2023-07-10 |
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bioconductor-mimosa
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public |
Mixture Models for Single-Cell Assays
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2023-07-10 |
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bioconductor-migsadata
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public |
MIGSA vignette data
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2023-07-07 |
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bioconductor-cssp
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public |
ChIP-Seq Statistical Power
|
2023-07-07 |
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bioconductor-sepira
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public |
Systems EPigenomics Inference of Regulatory Activity
|
2023-07-07 |
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bioconductor-clonality
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public |
Clonality testing
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2023-07-07 |
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bioconductor-savr
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public |
Parse and analyze Illumina SAV files
|
2023-07-07 |
