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2dimpute

Imputation in single cell RNA sequencing data using correlations from two dimensions

allelecount

Support code for NGS copy number algorithms

ampliconarchitect

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. This is development version. Please "watch" this repository for production release and methods manuscript soon.

ampliconclassifier

artificial-intelligence-deep-learning-machine-learning-tutorials

A comprehensive list of Deep Learning / Artificial Intelligence and Machine Learning tutorials - rapidly expanding into areas of AI/Deep Learning / Machine Vision / NLP and industry specific areas such as Automotives, Retail, Pharma, Medicine, Healthcare by Tarry Singh until at-least 2020 until he finishes his Ph.D. (which might end up being inter-stellar cosmic networks! Who knows! 😀)

ascat

ASCAT copy number R package

ascat.sc

ascatngs

Somatic copy number analysis using paired end sequencing

atacflow

An ATAC-seq pipeline wrapped in NextFlow that can be run by Jupyter

bamutils

bccmodels

Source files for DREAM7 BCC models

bggn213_f20

Fall 2020 BGGN-213 class website

bggn213_w21

Winter 2021 BGGN-213 class website

bimm143_classwork_w20

bimm143_f20

Undergraduate Laboratory Course in Bioinformatics Fall 2020

bimm143_s21

Undergraduate Laboratory Course in Bioinformatics Spring 2021

bimm143_w20

bioinformatics-ca.github.io

repository for student workshop pages

bioitworld2017

Notebooks and data for BioIT World 2017 Workshop

biomedicalresearch2019

Course Materials for EN.601.452 / AS.020.415 Computational Biomedical Research & Advanced Biomedical Research

bionitio-cpp

Demonstrating best practices for bioinformatics command line tools

blacklist

Application for making ENCODE Blacklists

brca-lrseq-pipeline

Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.

cafr

Attractor finding algorithm

cbw_htseq_module5

CBW HT-seq workshop module 5 on SV variants calling

cellcount

A Convolutional Neural Network for Segmenting and Counting Cells in Microscopy Images

cgp-somatic-docker

Dockerised and simplified version of SeqWare-CGP-SomaticCore

cgpbincounts

Generates bin count files as required by PICNIC-NGS and some other tools

chia-dropbox

add support to SRRxxx fastq.

chia-view

20191127