Noah Yu Zhang's repositories
acfs
A pipeline for de novo circRNA identification
bedops
:microscope: BEDOPS: high-performance genomic feature operations
branchpointer
prediction of intronic splicing branchpoints
CircMarker
Circular RNA Detection Tool
CircView
Sample-specific CircRNA Viewer
cs228-material
Teaching materials for the probabilistic graphical models and deep learning classes at Stanford
CSI
Complementary Sequence Index (CSI)
DCC
DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
deeplearningbook-chinese
Deep Learning Book Chinese Translation
find_circ
tools to find circRNAs in RNA-seq data
FUCHS
FUCHS - FUll circle CHaracterization from rna-Seq
IRFinder
Detecting intron retention from RNA-Seq experiments
juncBASE
Junction Based Analysis of Splicing Events for RNA-Seq
KNIFE
Known and Novel IsoForm Explorer. Statistically based splicing detection for circular and linear isoforms
lariat
perl scripts to identify lariat reads from RNAseq data
mit-deep-learning-book-pdf
MIT Deep Learning Book in PDF format (complete and parts) by Ian Goodfellow, Yoshua Bengio and Aaron Courville
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
PROBer_from_pachterlab
PROBer: A general toolkit for analyzing sequencing-based ‘toeprinting’ assays
pybedtools
Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)
pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
python-machine-learning-book
The "Python Machine Learning" book code repository and info resource
PythonDataScienceHandbook
Jupyter Notebooks for the Python Data Science Handbook
scikit-learn
scikit-learn: machine learning in Python
sklearn_pycon2015
Materials for my Pycon 2015 scikit-learn tutorial.
sklearn_tutorial
Materials for my scikit-learn tutorial
splash
Scripts to analyze data from the SPLASH protocol for generating in vivo RNA interactome maps
splice_branchpoints
scripts for Machine-learning annotation of human splicing branchpoints
STAR
RNA-seq aligner
yass
genomic alignment similarity search tool