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# Bioinformatics Workbook
## Table of Contents
### Introduction
* [Introduction to Bioinformatics](introduction/introduction.md)
* Introduction to Bioinformatics Terminology
* [Reads, Contigs, and Scaffolds](/introduction/dataTerminology.md)
* [Introduction to File Formats](introduction/fileFormats.md)
* [What is a Quality Score?](introduction/fastqquality-score-encoding.md)
### Experimental Design
* [Introduction to Experimental Design](experimentalDesign/eD_introduction.md)
* [Generic Examples of Experimental Design](/experimentalDesign/eD_genericExamples.md)
### Data Acquisition
* [Introduction to Data Acquisition](dataAcquisition/dAc_introduction.md)
* Transferring Data
* [Downloading with wget](dataAcquisition/FileTransfer/downloading-files-via-wget.md)
### Data Wrangling
* FASTA(Q) Manipulations
* [Determine Sequence Lengths](dataWrangling/fastaq-manipulations/calculate-sequence-lengths-in-a-fasta-file.md)
* [Converting FASTQ to FASTA](dataWrangling/fastaq-manipulations/converting-fastq-format-to-fasta.md)
* [Extract Sequences by Sequence ID](dataWrangling/fastaq-manipulations/retrieve-fasta-sequences-using-sequence-ids.md)
* Microsoft Excel Tips and Tricks
* [Create Workbook from Multiple Text Files](dataWrangling/microsoftExcel/export-multiple-worksheets-as-separate-text-files-in-excel.md)
* [Create Text Files from Workbook with Multiple Worksheets](dataWrangling/microsoftExcel/export-multiple-worksheets-as-separate-text-files-in-excel.md)
* [Create Index for All Worksheets](dataWrangling/microsoftExcel/generate-index-sheet-linking-all-spreadsheets-in-excel.md)
* Data Management
* [Deposition of Data to NCBI SRA](dataWrangling/NCBI_Data_Submission.md)
### Data Analysis
* Alignment
* [Blast Command Line Basic Example](dataAnalysis/blast/blastExample.md)
* Comparative Genomics
* [Gene Orthology, Synteny, and Visualization with Opscan, Iadhore, and Circos](dataAnalysis/ComparativeGenomics/Gene_Orthology_And_Synteny.md)
* [Gene Orthology, Synteny, and Visualization with Orthofinder, Iadhore, and Circos](dataAnalysis/ComparativeGenomics/OrthofinderSynteny.md)
* [Gene Overlap Significance Testing with R Gene_overlap Package](dataAnalysis/ComparativeGenomics/Gene_Category_Overlap_Fishers_exact_testing.md)
* [Phylostratiography: determining the LCA of all genes in a genome](dataAnalysis/ComparativeGenomics/phylostratr.md)
* Metagenomics
* [Intro to Metagenomics](dataAnalysis/Metagenomics/MetagenomicsP1.md)
* [Qiime2](dataAnalysis/Metagenomics/Qiime2.md)
* [DADA2](dataAnalysis/Metagenomics/Dada2.md)
* Genomic Repeat Identification
* [Helitron Identification in a Genome Sequence](dataAnalysis/ComparativeGenomics/Helitron_Scanner.md)
* [DNA Transposon Annotation with Inverted-Repeats Finder](dataAnalysis/ComparativeGenomics/InvertedRepeatsFinderForDNATransposonAnnotation.md)
* [LTR Retrotransposon Annotation with LTR-Finder](dataAnalysis/ComparativeGenomics/LTRFinder.md)
* [Repeat Annotation from Next-gen Sequencing Reads Using RepeatExplorer](dataAnalysis/ComparativeGenomics/RepeatExplorer.md)
* [De-novo Repeat Identification and Annotation from Genome Assemblies using RepeatModeler and RepeatMasker ](dataAnalysis/ComparativeGenomics/RepeatModeler_RepeatMasker.md)
* [Tandem Duplication Annotation in a Genome Assembly Using Mummer and RedTandem](dataAnalysis/ComparativeGenomics/Tandem_Duplication_Detection.md)
* Genome Assembly
* [GenomeScope to Estimate Genome Size](dataAnalysis/GenomeAssembly/genomescope.md)
* [Canu for Long Read Assembly](dataAnalysis/GenomeAssembly/LongRead/Canu.md)
* [Canu on XSEDE Bridges Machine](dataAnalysis/GenomeAssembly/LongRead/Canu_bridges.md)
* [Masurca with Pacbio and Illumina](dataAnalysis/GenomeAssembly/Hybrid/MaSuRCA.md)
* [Genome Scaffolding Using Synteny with Pyscaf](dataAnalysis/GenomeAssembly/Pyscaf_Synteny_Scaffolding.md): E. coli and Arabidopsis Genome Scaffolding
* Gene Annotation
* [Intro to Maker Gene Prediction](dataAnalysis/GenomeAnnotation/Intro_To_Maker.md)
* [Intro to Braker2 Gene Prediction](dataAnalysis/GenomeAnnotation/Intro_to_Braker2.md)
* [Motif Identification and Finding with MEME and FIMO](dataAnalysis/GenomeAnnotation/MEME_Motif_Finding_In_Genomes.md)
* [Assign GO Terms to Proteins using Deep Learning with DeepGoPlus](dataAnalysis/GenomeAnnotation/DeepGoPlus_AI_Functional_Prediction_of_Proteins.md)
* [How to identify the secreted protein from an annotation and predict subcellular localization](dataAnalysis/GenomeAnnotation/Secreted_Protein_Prediction_with_SignalP_and_TMHMM.md)
* [How to Functionally Classify Proteins using ProtTrans, a Kinase Example ](dataAnalysis/GenomeAnnotation/Protein_Classification_with_ProtTrans)
* RNA-Seq Analysis
* [RNA-Seq Example with a Genome Assembly](dataAnalysis/RNA-Seq/RNA-SeqIntro/RNAseq-using-a-genome.md): Arabidopsis with a Genome
* [RNA-Seq Example without a Genome Assembly](dataAnalysis/RNA-Seq/RNA-SeqIntro/RNAseq-without-a-genome.md): Arabidopsis without a Genome
* [Differential Expression Analysis](dataAnalysis/RNA-Seq/RNA-SeqIntro/Differential-Expression-Analysis.md): DESeq2
* Specialized Sequencing
* [ATAC-Seq](https://github.com/ISUgenomics/bioinformatics-workbook/blob/master/dataAnalysis/ATAC-seq/ATAC_tutorial.md) in Arabidopsis
### Data Visualization
* [Viewing Files Remotely without Transferring](Appendix/HPC/viewing-files-in-remote-machine-without-downloading-locally.md)
* [Creating Boxplots in R](dataWrangling/R/generate-boxplots.md)
* [Creating Heatmaps in R](dataWrangling/R/generate_heatmaps.md)
### Appendix
* Useful Programs
* [Introduction to GitHub](Appendix/github/introgithub.md)
* [Introduction to Slack](Appendix/slack.md)
* [How to use Markdown](Appendix/Markdown.md)
* Scripting and Command Line
* [Bioawk Basics](Appendix/Unix/bioawk-basics.md)
* [Introduction to Version Control and Github](Appendix/github/githubBasics.md)
* Installation
* [How to Install a Program?](Appendix/HPC/guide-for-installing-various-types-of-programs-in-linux.md)
* HPC
* Containers
* [Introduction to Containers](Appendix/HPC/Containers/Intro_Singularity.md)
* [Creating Containers using Singularity](Appendix/HPC/Containers/creatingContainers.md)
* [Modifying Existing Containers](Appendix/HPC/Containers/modifyingExistingContainers.md)
* SLURM
* [SLURM Cheatsheet](/Appendix/HPC/SLURM/slurm-cheatsheat.md)
* [SLURM Job Submission Dependencies](/Appendix/HPC/SLURM/submitting-dependency-jobs-using-slurm.md)
* PBS-Torque
* [Torque Cheatsheet](Appendix/HPC/pbstorque/submitting-dependency-jobs-using-pbs-torque.md)
* Miscellaneous
* [Password-less SSH](Appendix/HPC/password-less-ssh-login.md)
* [SSH Shortcuts](Appendix/HPC/ssh-shortcuts.md)
* Introduction to UNIX
* [Unix Basics 1](Appendix/Unix/unix-basics-1.md)
* [Unix Basics 2](Appendix/Unix/unix-basics-2admin.md)
* [Unix Basics 3 (grep)](Appendix/Unix/unix-basics-3grep.md)
* [Unix Basics 4 (sed)](Appendix/Unix/unix-basics-4sed.md)
* XSEDE
* [What is XSEDE, and How to Get an Allocation](Appendix/HPC/xsede/xsede.md)
* [Other Website Links of Interest](Appendix/OtherLinks.md)