Biocview "BiomedicalInformatics"

Accelerated similarity searching of small molecules

Analysis of alternative poly A site usage

Analysis of Brain Imaging Data

Analytical R tools for Mass Spectrometry

Analyze comorbidities from electronic health record data

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Ancestry Specific Allele Frequency Estimation

An R interface for computational modeling of tumor progression

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Application of gene classifiers

Assign Properties to TNBC Patients

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

A tool to identify potentially oncogenic genes

Automated functions for comparing various omic data from cbioportal.org

Automatic and interactive quality control for flow cytometry data

Automatic calculation of literature relevance of genes

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Cancer Variant Explorer

Cell birth and death rates estimation

Cheminformatics Toolkit for R

Clonogenic Survival Analysis in R made easy!

Clustering of Genomic Regions Analysis Method

Codon Usage Analysis and Prediction of Gene Expressivity

cytofkit2: an integrated mass cytometry data analysis pipeline. Cytofkit provides functions for data pre-processing, fast clustering, data visualization through linear or non-linear dimensionality reduction, automatic identification of cell subsets, and inference of the relatedness between cell subsets

cytofkit: an integrated mass cytometry data analysis pipeline

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Decomposition of individual tumors into mutational signatures by signature refitting

Delineate outstanding genomic zones of differential gene activity

Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients

Differential Expression Analysis for RNA-seq data through a robust variance component test

Differential gene usage in immune repertoires

Differentially Expressed Gene-Gene pairs

Discriminant Analysis for Evolutionary Inference

Drug-Target Interactions

Dual redundant reference sequencing

Dunedin Pace of Aging Methylation Score Calculator based on Dunedin Age 45 data (DunedinPACE)

Empirical Analysis of Digital Gene Expression Data in R

Estimate Systems Immune Response from RNA-seq data

EWCE for Multiple Gene Lists

Exposome exploration and outcome data analysis

Expression Weighted Celltype Enrichment

Find Causal Cell-Types Underlying Complex Trait Genetics

Functions for Cytoscape Automation

Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Genetic inteRaction and EssenTiality neTwork mApper

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

gwasurvivr: an R package for genome wide survival analysis

Identification and analysis of miRNA sponge interaction networks and modules

Identification and analysis of miRNA sponge regulation

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

immune Cell Analysis Tool

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Inferring miRNA sponge modules in heterogeneous data

Infers biological signatures from gene expression data

In-silico methods for genetic finemapping in inbred mice

Interact with the Broad Institute Cromwell workflow manager

Linear Models for Microarray Data

Longitudinal Analysis of Cancer Evolution (LACE)

Main Existing Human Datasets

Mismatch Tolerant Maximum Common Substructure Searching

Model-Based Comparative Analysis of the TCR Repertoire

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Multi-Scale Target Explorer

Multiview Intercellular SpaTial modeling framework

Muscle Epigenetic Age Test

Network Analysis Supported by Boosting

Network-based patient classifier

Optimal p-value weighting with independent information

Outlier Protein and Phosphosite Target Identifier

Package for CTDbase data query, visualization and downstream analysis

PatchseqMap

Patient Clonal Timescapes

Perform co-DE gene analysis

PhenoGeneRanker: A gene and phenotype prioritization tool

Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

Prediction of gestational age with Illumina HumanMethylation450 data

Protease Mapping

Protein Micro Array Data Management and Interactive Visualization

psygenet2r - An R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

Random Rotation Methods for High Dimensional Data with Batch Structure

Random walk with restart on multiplex and heterogeneous Networks

Reposition Drugs to Target Genes

'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

RImmPort: Enabling Ready-for-analysis Immunology Research Data

R interface to a subset of OpenBabel functionalities

R Interface to MELTING 5

R package for RIVER (RNA-Informed Variant Effect on Regulation)

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition

Signature-based Clustering for Diagnostic Purposes

Significance Analysis of Prognostic Signatures

Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems

Skeleton for library based on R6 class(es)

SparseSignatures

Spatial Image Analysis of Tissues

Spatial point data simulator for tissue images

ssPATHS: Single Sample PATHway Score

Suite of Functions for Pooled Crispr Screen QC and Analysis

Tools for Manipulating the FOBI Ontology

Tools for working with diverse immune genes

TRONCO, an R package for TRanslational ONCOlogy

Viral Evolution ReconStructiOn (VERSO)

Visual comparison of mutational processes in a set of tumors

Biocview "BiomedicalInformatics"

R Package Documentation

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