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DATA_SCIENCE_IN_BIOLOGY

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projects using galaxy, python, linux command line to analyze sequencing data

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## Tools for Data Science in Genomic Sequencing.

This repository includes projects using Python, R Language, Bioconductor, and Galaxy to understand, analyze, and interpret data from next-generation sequencing experiments.

The following projects are included:

#### 1. [Galaxy for Next Generation Sequencing](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Galaxy%20for%20Next%20Generation%20Sequencing)

Set up a workflow to analyse DNA polymorphic sites of father-mother-child sequencing samples

#### 2. [Python for DNA Sequencing Analysis](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Python%20for%20DNA%20Sequencing%20Analysis)

This project includes a set of tools for DNA sequence analysis
(

a. check records in file (count_records),
b. compute the length of each DNA sequence (check_length), 
c. identify open read frame in each DNA sequence (orf_identifier), 
d. identify repeated motif in sequence (repeats_identifier)
).

#### 3. [Linux Command Line Tools for Data Science in Biology](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Linux%20Command%20Line%20Tools%20for%20Data%20Science%20in%20Biology)

This project apply bowtie2, samtools, bedtools and bcftools to: 
1) Analyze RNA-seq data to determine sets of genes that are expressed in the various tissues; 
2) cataloging genetic variation using SAMtools and BEDtools as well as other Unix commands; 
3) develop a pipeline for variant calling in a given genome; 4) perform the bioinformatics analysis to determine genes that      are differentially expressed at different experimental conditions with Linux command line.

#### 4. [Sequencing Alignment and Genome Assembly](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Sequencing%20Alignment%20and%20Genome%20Assembly)

Python is used to implement key algorithms and data structures to analyze real genomes and DNA sequencing datasets.

#### 5. [R and Bioconductor](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Bioconductor%20for%20Genomic%20Analysis%20)

Use tools from the Bioconductor project and R programming language to analyze genomic data.

#### 6. [Statistics with R for Genomic Data](https://github.com/lanttern/DATA_SCIENCE_IN_BIOLOGY/tree/master/Statistics%20for%20Genomic%20Data%20Science)

An introduction to the statistics for analysis of genomic data.

DATA_SCIENCE_IN_BIOLOGY

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