qiutip

Jake Qiu's starred repositories

apples

distance based phylogenetic placement

Language:PythonGPL-3.02400

TreeSwift

TreeSwift: Fast tree module for Python 3

Language:PythonGPL-3.07500

nongenetic-evolution-of-tumor-subclones

Language:Python100

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.

Language:PythonNOASSERTION13100

samplot

Plot structural variant signals from many BAMs and CRAMs

Language:PythonMIT50400

SingleCheck

Language:Shell300

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?

CC0-1.09500

sonics

SONiCS - Stutter mONte Carlo Simulation

Language:CythonMIT300

scg_lib_structs

Collections of library structure and sequence of popular single cell genomic methods

Language:HTML40300

somaticIBD

Code supporting our manuscript "The mutational profile and clonal landscape of the inflammatory bowel disease affected colon"

Language:HTML600

snp-sites

Finds SNP sites from a multi-FASTA alignment file

Language:CNOASSERTION23100

OpticalPooledScreens

Code and examples for optical pooled screens (updated protocol).

Language:PythonMIT1100

RNA-seq-analysis

RNAseq analysis notes from Ming Tang

Language:PythonMIT85400

climbing-accidents

Analysis of 30 years of climbing accident reports

4100

sktime-tutorial-pydata-amsterdam-2020

Introduction to Machine Learning with Time Series at PyData Festival Amsterdam 2020

Language:Jupyter NotebookBSD-3-Clause12300

sktime

A unified framework for machine learning with time series

Language:PythonBSD-3-Clause760400

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

GPL-3.0144600

MML-Companion

This is a companion to the ‘Mathematical Foundations’ section of the book, Mathematics for Machine Learning by Marc Deisenroth, Aldo Faisal and Cheng Ong, written in python for Jupyter Notebook.

Language:Jupyter Notebook24000