SciComp8's repositories
NGSOmics_Programming
Computational biology/bioinformatics workflows, codes, tech & concept notes on NGS data
Python_Programming
Python codes related to medical artificial intelligence, machine learning, bioinformatics algorithms, and computer science for python programming, among others
Project_Portfolio
A portfolio of programming work affiliated with miscellaneous molecular and clinical research projects
Database_Programming
SQL database, Cloudant NoSQL database, LeetCode materials
R_Programming
Convenient programming in R
ascets
This repository contains the code to run the ASCETS arm-level copy number events caller for targeted sequencing data. ASCETS produces arm-level copy-number variant calls and arm-level weighted average log2 segment means from segmented copy number data.
atac-seq-pipeline
ENCODE ATAC-seq pipeline
bowtie2
A fast and sensitive gapped read aligner
cookiecutter
A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.
cookiecutter-data-science
A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
gatk
Official code repository for GATK versions 4 and up
GeomxTools
Tools for NanoString GeoMx Digital Spatial Profiler data for reading DCC and PKC files to NanoStringGeomxSet class, Normalization and QC.
GSEApy
Gene Set Enrichment Analysis in Python
Harvard_Bioinformatics_Knowledgebase
This is the bioinformatics knowledgebase from Harvard Chan Bioinformatics Core
hdWGCNA
High dimensional weighted gene co-expression network analysis
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
oncokb-annotator
Annotates variants in MAF with OncoKB annotation.
pattern_analysis
A package for analyzing patterns in biological data.
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
RIA
:exclamation: This is a read-only mirror of the CRAN R package repository. RIA — Radiomics Image Analysis Toolbox for Medial Images. Homepage: https://pubmed.ncbi.nlm.nih.gov/29233836/
sphinx
The Sphinx documentation generator
STAR
RNA-seq aligner
Tangram
Spatial alignment of single cell transcriptomic data.
vast-tools
A toolset for profiling alternative splicing events in RNA-Seq data.