lux563624348

Bioinformatics

HiC_Hubs

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

Optimization_problem_BFGS

TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Algorithm_JAVA

Com-Phy

HW

CS_Learning

Spatial_analysis_Kriging

biotech

CRISPRme_gnomAD

diffexpr

Porting DESeq2 and DEXSeq into python via rpy2

HPC_colonial_one

IgA_Tianyi

Data_mining

investment_research

kaggle-quora-question-pairs

My solution to Kaggle Quora Question Pairs competition (Top 7%, 209th of 3307).

lux563624348.github.io

nextflow

Some projects in nextflow

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Python_Learn

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnatoy

A proof of concept RNA-Seq pipeline with Nextflow

RPA-Python

Python package for doing RPA

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

sec_review

A real world full-stack application using LlamaIndex

SISG2018

Materials for UW SISG Module 4

social_network

StarSpace

Learning embeddings for classification, retrieval and ranking.