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5years

affyqc_module

Affymetrix microarrays of different technology versions are very often used in transcriptomics analysis. Quality control and normalization approaches do exist, especially as packages in Bioconductor/R. However: -Procedures are often different between teams. -They are not always easy to access as they run through command lines. -It is often not clear what the meaning of the specific settings and results are -They are not always usable for the newer technology types of arrays. To tackle this, we proposed an automated well-documented and user-friendly pipeline for Affymetrix microarray quality control and normalization.

agilent

Microarray analysis of agilent data

beautiful-visualization-with-r

《R语言数据可视化之美》配套代码

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

cardiac-metabolic-reprogramming-analysis-of-tof

Cardiac Metabolic Reprogramming Analysis of ToF

chip-seq

circlize

Circular visualization in R

cmscaller

cnv

complexheatmap

Make Complex Heatmaps

covid_balf

R script for the covid balf data analysis

datasubsidiary

UBC9 promotes KRAS mutation colorectal cancer development through the activation of TGF-beta signaling

deep-learning

deepcpg

Deep neural networks for predicting CpG methylation

dna-me-pipeline

DCC/DAC methylation pipeline source

dna-methylation-analysis

DNA methylation analysis notes from Ming Tang

dockerfile_jupyter

eat-bio-analysis

enrichedheatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.

epidish

This package contains a reference-based function to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.

esatac

Bioconductor package: An Easy-to-use Systematic pipeline for ATACseq data analysis

featureselection

Feature Selection in R using glmnet-lasso, xgboost and ranger

geo

glmnet

R package glmnet for estimating lasso and elastic net

gseabase

Gene set enrichment data structures and methods

gtrellis

Genomic plot in trellis layout

humanid

my first R package just for testing

illumina450k-methylation

From IDAT to beta.

ilmnqc_module

R code for the Illumina preprocessing and QC module for ArrayAnalysis.org