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tidymodules
An Object-Oriented approach to Shiny modulesYADA
Open-source Data Opspeax
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoderstorchsurv
Deep survival analysis made easyscar
scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omicscellxgene-gateway
Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.ontobrowser
OntoBrowser is a web-based application for managing ontologiesyap
High throughput, pain-free big data pipelines.pQSAR
Massively multitask stacked model for predicting activity of thousands of biological assaysChemBioMultimodalAutoencoders
a package for streamlined multidomain data integration and translation based on cross-modal autoencoders architecturespqsar2cpd
pqsar2cpd is a deep learning algorithm for translation of activity profiles into novel molecules.easyTrackHubs
This package provides a function to reformat lists of genome coverage files, such as bigWig of bam files, into the directory structure of a UCSC Track Hub ready to be visualized in the genome browser. For details about it's use, please have a look at the vignette of the package.pisces
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.JAEGER
JAEGER is a deep generative approach for small-molecule designxgx
Exploratory Graphics for PKPD dataCausal-inference-in-RCTs
This repository contains code examples for several methods in a Causal Inference in RCTs short course.patprofile
Standard patient profile for shiny appsDRUG-seq
DRUG (Digital RNA with pertUrbation of Genes)-seq data analysis pipelineMoaBox
A repository of compound-target annotations in support of Systematic Chemogenetic Library Assemblyrailroadtracks
Railroadtracks is a Python package to handle connected computation steps for DNA and RNA Seq.gridvar
GridVar is a jQuery plugin that visualizes multi-dimensional datasets as layers organized in a row-column format.xgxr
R package for supporting exploratory graphics at http://opensource.nibr.com/xgxJenkins-LSCI
Jenkins for Life Science Continuous Integrationgranulator
EQP-cluster
Unix-based RNA-seq quantification pipelinemdx-utils
AEGIS
MHC-II presentation predictorhpath
An ontology of histopathological morphologieshabitat
"Where files live" - Simple object management system using AWS S3 and Elasticsearch Service to manage objects and their metadataRBesT
Tool-set to support Bayesian evidence synthesis in RscRNAseq_workflow_benchmark
Workflow for the analysis fo single-cell RNASeq data using R/bioconductordiv_rank
This code allows is for diversity picking across multiple different, and potentially overlapping chemical compound classes, while at the same time optimizing a property score. This algorithm has been used in the re-design of the Novartis screening deck as described in https://dx.doi.org/10.1021/acs.jmedchem.0c01332subpat
{subpat} is a collection of modules to create subpopulations and subgroups from clinical trial dataAdvanced-User-Interfaces-for-Shiny-Developers
UMM-Discovery
UMM-Discovery is a fully unsupervised deep learning method to cluster cellular images with similar phenotypes together, solely based on the intensity values.toolscore
Script and example data for "Evidence-Based and Quantitative Prioritization of Tool Compounds in Phenotypic Drug Discovery"UNIQUE
A Python library for benchmarking uncertainty estimation and quantification methods for Machine Learning models predictionsMOBER
Multi-omics batch effect remover methodhdf5r
CellSIUS
CellSIUS: Cell Subtype Identification from Upregulated gene Setsdms-pipeline
Snakemake pipeline for quantification of deep mutational scanning (DMS) data from overlapping paired-end reads in fastq files from amplicon sequencingNDSRIs_in_silico_tool
N-nitrosamine Autonomous Carcinogenic Potency Categorization Approach Calculation Toolchraw
The package analyzes chromatin and multi-omic experiments. It extends the MultiAssayExperiment object and builds a ChrawExperiment object from ENCODE’s output. It performs QC plotting, identifies differential events and other functionalities. More details in package vignettes.Project-Mona-Lisa
Project Mona Lisa (PML): Machine-learning Assisted Diagramming PlatformpeakCombiner
The fully R based tool peakCombiner is a user-friendly, transparent, modular and customizable package with the purpose to create a consensus peak file from genomic input regions. The aim is to allow even novice R users to create good quality combined peak sets to be used as the starting point for most downstream differential analyses.verifyr
A package to hold R functions for comparing different version of clinical trial TLFsTRAWLING
Description: Build TRAWLING: a Transcriptome Reference AWare of spLicING eventsTAT
Transcriptomics-to-Activity Transformer (TAT) is a deep learning model to predict compound bioactivity in a dose-response assay using compound-induced transcriptomic profiles over concentration.nxc-chess
watMD
Water tool for molecular dynamics that calculates solvation fields for interaction between water and non-solvant moleculessolid-tumor-CHIP
Clonal hematopoiesis detection in cancer patients using cell free DNA sequencingNovartis.github.io
Public gallery of NIBR Open Source projectssidtoolbox
Subgroup identification toolboxProfile-QSAR
Massively multitask stacked model for predicting activity of thousands of biological assaysCu-Catalyzed-Ligands-Design
By establishing machine learning (ML) models, the design of ligands and optimization of reaction conditions were effectively facilitatedEQP-QM
Unix based RNA-seq quantification moduleGreyChemicalMatter
A pipeline to identify bioactive small molecules with likely novel modes of actions and dynamic SAR from historic cell-HTS profiles, with an example application and hitlist from PubChem datamvAC50
AC50 potencies from multivariate assay readouts like gene signatureschess-redux
mueller_et_al_2018
Processed data relating to Continuous monitoring of patient mobility for 18 months using inertial sensors following traumatic knee injury: a case study Mueller A., Hoefling H., Nuritdinow T., et al. Paper: http://doi.org/10.1159/000490919 Raw data: http://doi.org/10.5281/zenodo.1443190Love Open Source and this site? Check out how you can help us