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Package Name Access Summary Updated
bioconductor-hdxmsqc public An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments 2024-12-21
bioconductor-tcgabiolinks public TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data 2024-12-21
bioconductor-tomoda public Tomo-seq data analysis 2024-12-21
bioconductor-phenopath public Genomic trajectories with heterogeneous genetic and environmental backgrounds 2024-12-21
bioconductor-dominosignal public Cell Communication Analysis for Single Cell RNA Sequencing 2024-12-21
bioconductor-metnet public Inferring metabolic networks from untargeted high-resolution mass spectrometry data 2024-12-21
bioconductor-goexpress public Visualise microarray and RNAseq data using gene ontology annotations 2024-12-21
bioconductor-lionessr public Modeling networks for individual samples using LIONESS 2024-12-21
bioconductor-cnvranger public Summarization and expression/phenotype association of CNV ranges 2024-12-21
bioconductor-oncoscore public A tool to identify potentially oncogenic genes 2024-12-21
bioconductor-pgxrpi public R wrapper for Progenetix 2024-12-21
bioconductor-omicsprint public Cross omic genetic fingerprinting 2024-12-21
bioconductor-ppinfer public Inferring functionally related proteins using protein interaction networks 2024-12-21
bioconductor-pepsettest public Peptide Set Test 2024-12-21
bioconductor-iggeneusage public Differential gene usage in immune repertoires 2024-12-21
bioconductor-surfaltr public Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr 2024-12-21
bioconductor-immunogenviewer public Visualization and evaluation of protein immunogens 2024-12-21
bioconductor-rscudo public Signature-based Clustering for Diagnostic Purposes 2024-12-21
bioconductor-kmcut public Optimized Kaplan Meier analysis and identification and validation of prognostic biomarkers 2024-12-21
bioconductor-padma public Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis 2024-12-21
bioconductor-mousefm public In-silico methods for genetic finemapping in inbred mice 2024-12-21
bioconductor-coregx public Classes and Functions to Serve as the Basis for Other 'Gx' Packages 2024-12-21
bioconductor-nipalsmcia public Multiple Co-Inertia Analysis via the NIPALS Method 2024-12-21
bioconductor-gemma.r public A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses 2024-12-21
r-dinamic.duo public In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. A manuscript based on DiNAMIC.Duo is currently under development. 2024-12-21
bioconductor-hipathia public HiPathia: High-throughput Pathway Analysis 2024-12-21
bioconductor-aldex2 public Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account 2024-12-21
r-cimpl public No Summary 2024-12-21
bioconductor-msfeatures public Functionality for Mass Spectrometry Features 2024-12-21
bioconductor-qfeatures public Quantitative features for mass spectrometry data 2024-12-21
bioconductor-bioga public Bioinformatics Genetic Algorithm (BioGA) 2024-12-21
bioconductor-omicspcadata public Supporting data for package OMICsPCA 2024-12-21
bioconductor-swath2stats public Transform and Filter SWATH Data for Statistical Packages 2024-12-21
bioconductor-survtype public Subtype Identification with Survival Data 2024-12-21
bioconductor-repviz public Replicate oriented Visualization of a genomic region 2024-12-21
bioconductor-midashla public R package for immunogenomics data handling and association analysis 2024-12-21
bioconductor-qtlexperiment public S4 classes for QTL summary statistics and metadata 2024-12-21
bioconductor-nanomethviz public Visualise methylation data from Oxford Nanopore sequencing 2024-12-21
bioconductor-isobar public Analysis and quantitation of isobarically tagged MSMS proteomics data 2024-12-21
bioconductor-brgedata public Exposures, Gene Expression and Methylation data for ilustration purpouses 2024-12-21
bioconductor-multimodalexperiment public Integrative Bulk and Single-Cell Experiment Container 2024-12-21
bioconductor-chihaya public Save Delayed Operations to a HDF5 File 2024-12-21
bioconductor-cellscore public Tool for Evaluation of Cell Identity from Transcription Profiles 2024-12-21
bioconductor-chromplot public Global visualization tool of genomic data 2024-12-21
bioconductor-intercellar public InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics 2024-12-21
bioconductor-missrows public Handling Missing Individuals in Multi-Omics Data Integration 2024-12-21
bioconductor-supersigs public Supervised mutational signatures 2024-12-21
r-noisyr public Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output. 2024-12-21
bioconductor-gdrutils public A package with helper functions for processing drug response data 2024-12-21
bioconductor-lace public Longitudinal Analysis of Cancer Evolution (LACE) 2024-12-21
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