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2020starprotocols_pipeline

This is the pipeline of 2020 STAR Protocols

alignsnpprimertogene

align snp primers to a specific genomic gene sequence

atpolydb

Atwell et al data

awesome-single-cell

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

bio-vcf

Smart VCF parser DSL

bioxm2.7

bs-seq_functions

some R and python scripts for BS-seq(Whole-genome bisulfite sequencing)

coursera-bioinformatics

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)

coursere_bioinformatics_specialization

cris

Find CRISPR binding sites

deep-learning-with-python-notebooks

Jupyter notebooks for the code samples of the book "Deep Learning with Python"

deeplearning-with-python

notebook scripts for deepping learning with python

deeptools

Tools to process and analyze deep sequencing data.

deseq2

Differential gene expression analysis based on the negative binomial distribution

genomics_general

General tools for genomic analyses.

genotype-files-manipulations

Set of scripts to manupulate tab-delimited genotype calls files as well as to convert calls-files to other popular formats.

ggsashimi

Command-line tool for the visualization of splicing events across multiple samples

hisat2

Graph-based alignment (Hierarchical Graph FM index)

imputer

Impute GBS genotype

kalman-and-bayesian-filters-in-python

Kalman Filter book using Jupyter Notebook. Focuses on building intuition and experience, not formal proofs. Includes Kalman filters,extended Kalman filters, unscented Kalman filters, particle filters, and more. All exercises include solutions.

learns4

S4 class in R

machinelearningwithpython

miscwork

multipool

High-resolution genetic mapping for pooled sequencing.

pybsaseq

A novel algorithm for BSA-Seq data analysis

qqman

R code for creating Manhattan plots and Q-Q plots for GWAS

qtlseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

re-searcher

"re-Searcher" is a toolbox aimed to simplify the task for genomics data mining from big VCF files.

rna_seq_functions

some scripts and pipelines for analysis RNA-seq

rodeo

A data science IDE for Python