Pengfei Xu's repositories
awesome-single-cell
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
Bioinformatics-Resources
A curated list of resources for learning bioinformatics.
ANTsRNet
Medical image analysis framework merging ANTsR and deep learning
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome-biological-visualizations
A list of web-based interactive biological data visualizations.
awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
awesome-reproducible-research
A curated list of reproducible research case studies, projects, tutorials, and media
CAMTHC
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
CaPTk
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
ClustAssess
A set of tools for assessing clustering robustness
ChatPaper
Use ChatGPT to summarize the arXiv papers. 全流程加速科研，利用chatgpt进行论文总结+润色+审稿+审稿回复
Data-Analysis
Data Science Using Python
DNAm-based-age-predictor
A chronological age predictor based on DNA methylation
EstimateClonality
Forked from https://bitbucket.org/nmcgranahan/pancancerclonality/src/master/.
Gene-expression-deconvolution
Gene expression deconvolution
genomepy
Download and use genomes the easy way.
getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
GSgalgoR
An evolutionary Algorithm for the Identification and Study of Prognostic Gene Expression Signatures in Cancer (Bioconductor)
marchionni_projects
Collaboration with Luigi Marchionni (JHU) and RIKEN with recount2 data
msisensor2
Microsatellite instability (MSI) detection for tumor only data.
Radiology
Python Codes that help to manage medical images for Machine Learning
RadiomicsFeatureVisualization
Visualization for radiomics feature generated by pyradiomics
scSigR
Generate signature matrix from single cell data.
TCGAmutations
R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)
TMwR
Code and content for "Tidy Modeling with R"
trackplot
Generate IGV style locus tracks from bigWig files in R