bioconductor-deseq2
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public |
Differential gene expression analysis based on the negative binomial distribution
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2024-12-27 |
bioconductor-buscorrect
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public |
Batch Effects Correction with Unknown Subtypes
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2024-12-27 |
bioconductor-scuttle
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public |
Single-Cell RNA-Seq Analysis Utilities
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2024-12-27 |
bioconductor-apeglm
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public |
Approximate posterior estimation for GLM coefficients
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2024-12-27 |
bioconductor-mbkmeans
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public |
Mini-batch K-means Clustering for Single-Cell RNA-seq
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2024-12-27 |
bioconductor-biocsingular
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public |
Singular Value Decomposition for Bioconductor Packages
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2024-12-27 |
bioconductor-monocle
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public |
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
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2024-12-27 |
bracken
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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.
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2024-12-27 |
bioconductor-ioniser
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public |
Quality Assessment Tools for Oxford Nanopore MinION data
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2024-12-27 |
bioconductor-systempiper
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public |
systemPipeR: Workflow Environment for Data Analysis and Report Generation
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2024-12-26 |
bioconductor-rsvsim
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public |
RSVSim: an R/Bioconductor package for the simulation of structural variations
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2024-12-26 |
bioconductor-dada2
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public |
Accurate, high-resolution sample inference from amplicon sequencing data
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2024-12-26 |
bioconductor-eatonetalchipseq
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public |
ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010
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2024-12-26 |
bioconductor-sevenc
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public |
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
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2024-12-26 |
r-gkmsvm
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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.
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2024-12-26 |
bioconductor-wiggleplotr
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public |
Make read coverage plots from BigWig files
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2024-12-26 |
bioconductor-plyranges
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public |
A fluent interface for manipulating GenomicRanges
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2024-12-26 |
bioconductor-dmchmm
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public |
Differentially Methylated CpG using Hidden Markov Model
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2024-12-26 |
bioconductor-chipenrich.data
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public |
Companion package to chipenrich
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2024-12-26 |
r-easylift
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public |
A convenience package for converting between popular mouse & human builds.
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2024-12-26 |
bioconductor-roar
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public |
Identify differential APA usage from RNA-seq alignments
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2024-12-26 |
bioconductor-seqsetvis
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public |
Set Based Visualizations for Next-Gen Sequencing Data
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2024-12-26 |
bioconductor-hitc
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public |
High Throughput Chromosome Conformation Capture analysis
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2024-12-26 |
bioconductor-consensusseeker
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public |
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
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2024-12-26 |
bioconductor-rifi
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public |
'rifi' analyses data from rifampicin time series created by microarray or RNAseq
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2024-12-26 |
bioconductor-r3cseq
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public |
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
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2024-12-26 |
bioconductor-chromheatmap
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public |
Heat map plotting by genome coordinate
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2024-12-26 |
bioconductor-excluster
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public |
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
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2024-12-26 |
bioconductor-rificomparative
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public |
'rifiComparative' compares the output of rifi from two different conditions.
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2024-12-26 |
bioconductor-pram
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public |
Pooling RNA-seq datasets for assembling transcript models
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2024-12-26 |
bioconductor-scanvis
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public |
SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions
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2024-12-26 |
bioconductor-hicvenndiagram
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public |
Venn Diagram for genomic interaction data
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2024-12-26 |
bioconductor-ideoviz
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public |
Plots data (continuous/discrete) along chromosomal ideogram
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2024-12-26 |
bioconductor-tidycoverage
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public |
Extract and aggregate genomic coverage over features of interest
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2024-12-26 |
r-immucellaimouse
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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.
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2024-12-26 |
bioconductor-normr
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public |
Normalization and difference calling in ChIP-seq data
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2024-12-26 |
bioconductor-hicaggr
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public |
Set of 3D genomic interaction analysis tools
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2024-12-26 |
r-sigqc
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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.
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2024-12-26 |
bioconductor-dmcfb
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public |
Differentially Methylated Cytosines via a Bayesian Functional Approach
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2024-12-26 |
bioconductor-epidecoder
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public |
epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
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2024-12-26 |
bioconductor-motifdb
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public |
An Annotated Collection of Protein-DNA Binding Sequence Motifs
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2024-12-26 |
bioconductor-scpipe
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public |
Pipeline for single cell multi-omic data pre-processing
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2024-12-26 |
bioconductor-coverageview
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public |
Coverage visualization package for R
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2024-12-26 |
bioconductor-metagene2
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public |
A package to produce metagene plots
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2024-12-26 |
bioconductor-syntenet
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public |
Inference And Analysis Of Synteny Networks
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2024-12-26 |
bioconductor-past
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public |
Pathway Association Study Tool (PAST)
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2024-12-26 |
bioconductor-gseabenchmarker
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public |
Reproducible GSEA Benchmarking
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2024-12-26 |
r-geneexpressionfromgeo
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public |
A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.
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2024-12-26 |
bioconductor-rarr
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public |
Read Zarr Files in R
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2024-12-26 |
bioconductor-enrichmentbrowser
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public |
Seamless navigation through combined results of set-based and network-based enrichment analysis
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2024-12-26 |