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2016

Course material for BIO 260 and CSCI E-107 in Spring 2016

2016_data

repository for data for Spring 2016

access-pipeline

cfDNA Sequencing Pipeline with UMI

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

biometrics

Python package to calculate various sample contamination metrics.

cancer-type-prediction-from-tumour-dna

caveman

SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

cbs

A simple implementation of the circular binary segmentation algorithm in python

cheatsheets-ai

Essential Cheat Sheets for deep learning and machine learning researchers https://medium.com/@kailashahirwar/essential-cheat-sheets-for-machine-learning-and-deep-learning-researchers-efb6a8ebd2e5

cmo

Modular bioinformatics pipelines for the CMO

cnv_simulator

CNV simulation scripts and meta data

cnvkit

Copy number variant detection from targeted DNA sequencing

cs224n-2019-solutions

Complete solutions for Stanford CS224n, winter, 2019

cs224n-assignments

My solutions to the practical assignments of CS224n (Natural Language Processing with Deep Learning) [Stanford University-Winter 2019]

cs224n-natural-language-processing-with-deep-learning

data

Repository for data in datasciencelabs

dataminingapp-lectures

Official content for the Spring 2015 Boston University CS591 "Tools and Techniques for Data Mining and Applications" course

deletion_phenotype

Disease phenotype association with deletion and their locations

ensembl-vep

The Variant Effect Predictor predicts the functional effects of genomic variants

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

genome-nexus

Interpreting cancer genomics data

genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API

getbasecountsmultisample

hts_solid_preprocessing

Archive of the SOLiD preprocessing scripts by Ariella Sasson & Todd Michael originally hosted at http://hts.rutgers.edu/filter

igv-reports

Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.

lancet

Microassembly based somatic variant caller for NGS data

learn_nlp_again

Solutions and algorithms for Speech and Language Processing (3rd ed. draft)

lollipopplot

JavaScript mutation needle plot

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.