liuxch5's repositories
shinyNgsreports
The shiny app that accompanies the ngsReports R package
CiteFuse
CiteFuse:
STOPGAP
Scripts for generating integrated dataset from publically available data sources to evaluate known genetic associations evidence of varying disease areas and supporting information. The integrated dataset is also included.
CIPR-Shiny
Repository for Shiny implementation of CIPR
clustergrammer
An interactive heatmap visualization built using D3.js
varanto
Varanto is an online database and tool for annotating human genetic variations using various annotation data sources.
ATLANTiC
Integrated analysis of genomes, transcriptomes, proteomes and drug responses of cancer cell lines (CCLs) is an emerging approach to uncover molecular mechanisms of drug action. We extend this paradigm to measuring proteome activity landscapes by acquiring and integrating quantitative data for 10,000 proteins and 55,000 phosphorylation sites (p-sites) from 125 CCLs. These data are used to contextualize proteins and p-sites and predict drug sensitivity. For example, we find that Progesterone Receptor (PGR) phosphorylation is associated with sensitivity to drugs modulating estrogen signaling such as Raloxifene. We also demonstrate that Adenylate kinase isoenzyme 1 (AK1) inactivates antimetabolites like Cytarabine. Consequently, high AK1 levels correlate with poor survival of Cytarabine-treated acute myeloid leukemia patients, qualifying AK1 as a patient stratification marker and possibly as a drug target. We provide an interactive web application termed ATLANTiC (http://atlantic.proteomics.wzw.tum.de), which enables the community to explore the thousands of novel functional associations generated by this work.
presentations
A central repository of Business Science presentations
chordomics
Interactive visualisation and data annotation for meta-omics data
Adjutant
Runs a pubmed query, returns results and allows user to explore high-level structure of returned documents
musica
MuSiCa - Mutational Signatures in Cancer
shinyCyJS
cytoscape.js R binding library for shiny
TSIS
TSIS: an R package to infer time-series isoform switch of alternative splicing
PatientExploreR
Dynamic visualization of Electronic Health Record data in the OMOP framework
V-SVA
V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data
UpSetR
An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..
ggplotwithyourdata
R Shiny app as an inteface to ggplot2
pwc
Papers with code. Sorted by stars. Updated weekly.
netGO
R/Shiny package for network-integrated pathway enrichment analysis
metabridge_shiny
🕸 Network-based multi-omic integration of metabolomics data.
DNA_Rchitect
A Shiny App for visualizing genomic data
tarpan
TarPan Viewer
EDGE-in-TCGA
Source code to reproduce results from "Exploring Drivers of Gene Expression in The Cancer Genome Atlas" by Rau et al. (2017)
ddPCRclust
A package for automated quantification of non-orthogonal, multiplexed ddPCR data
iS-CellR
iS-CellR: interactive graphical tool for analysis of single-cell RNAseq data
morpheus.R
R interface to morpheus.js heatmap widget
checkMyIndex
Search for a set of compatible indexes for your sequencing experiment
pavian
🌈 Interactive analysis of metagenomics data