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awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

biobambam2

Tools for early stage alignment file processing

bitcoin-price-prediction

Bayesian regression for latent source model and Bitcoin

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

cafe

aCcelerated Alignment-FrEe sequence analysis

cidr

Clustering through Imputation and Dimensionality Reduction

clipumi

Detection and Removal of initial UMI Tags from FASTQ Files

d-gex

Deep learning for gene expression inference

data_hacks

Command line utilities for data analysis

ddia

《Designing Data-Intensive Application》DDIA中文翻译

deep-neural-networks-healthcare

Tangible and Practical Deep Learning Projects Repository for Healthcare such as Cancer, Drug Discovery, Genomic and More

deepcpg

Deep neural networks for predicting CpG methylation

deeplearning-biology

A list of deep learning implementations in biology

dlwpt-code

Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.

falconn

FAst Lookups of Cosine and Other Nearest Neighbors (based on fast locality-sensitive hashing)

frmc

FRMC is a fast and robust imputation software for single cell RNA-Seq data.

ginkgo

Cloud-based single-cell copy-number variation analysis tool

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

hap.py

Haplotype VCF comparison tools

hapcut2

software tools for haplotype assembly from sequence data

hcmb

This is an an algorithm, Hi-C Matrix Balancing (HCMB), based on iterative solution of equations, combining with linear search and projection strategy to normalize the hi-C original interaction data.

hla

xHLA: Fast and accurate HLA typing from short read sequence data

hotstarting-for-star-alignment

A hot-starting method for STAR Alignment.

introtoml

kmer

Alignment-free algorithm to correlate genetic sequences.

loftee

lshash

A fast Python implementation of locality sensitive hashing.

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

metapi

A general metagenomics data mining system focus on robust microbiome research