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Added all of my GitLab repository, now I'm linking from there to this place
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‎extras/articles.md

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# Bioinformatics - Extra Resources
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# Articles
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1. [So you want to be a computational biologist?](http://www.nature.com/nbt/journal/v31/n11/full/nbt.2740.html) by Nick Loman and Mick Watson (2013).
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1. [A Quick Guide for Developing Effective Bioinformatics Programming Skills](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000589) by Joel Dudley and Atul Butte (2009).
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1. [Unix Philosophy](https://en.wikipedia.org/wiki/Unix_philosophy)

‎extras/free-books.md

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# Bioinformatics - Extra Resources
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# Free Books
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* [Molecular Biology of the Cell](https://www.ncbi.nlm.nih.gov/books/NBK21054/)
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* [An Introduction to Genetic Analysis](https://www.ncbi.nlm.nih.gov/books/NBK21766/)
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* [The GNU/Linux Command Line Interface (CLI)](http://linuxcommand.org/tlcl.php)
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* [Unix Grymoire](http://www.grymoire.com/)
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* [Algorithms and Data Structures](http://interactivepython.org/runestone/static/pythonds/index.html)
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* [Think like a Computer Scientist](http://interactivepython.org/runestone/static/thinkcspy/index.html)
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## Language Books
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* [Python](http://scipy.org/topical-software.html)
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* [Interactive Py](http://interactivepython.org/runestone/static/pythonds/index.html)
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* [Py For Biologists](http://pythonforbiologists.com/index.php/introduction-to-python-for-biologists/)
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* Perl
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* [Perl 6](http://perl6intro.com/)
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* [Unix and Perl for Biologists](http://korflab.ucdavis.edu/Unix_and_Perl/index.html)
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* [Haskell](http://learnyouahaskell.com/chapters)
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* [Julia](http://julialang.org/learning/) ([book](https://en.wikibooks.org/wiki/Introducing_Julia))
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* [Make](http://www.oreilly.com/openbook/make3/book/index.csp) pipelines

‎extras/free-courses.md

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PH525.6x: High-performance computing for reproducible genomics
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PH525.7x: Case studies in functional genomics
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## Workshops and tutorials mostly:
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* [Data Carpentry](http://www.datacarpentry.org/lessons/)
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* [OpenHelix](http://www.openhelix.com/freeTutorials.cgi)
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* [BioStars](https://www.biostars.org/t/Tutorials/)
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* [GenomeSpace Recipes](http://recipes.genomespace.org/home)
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* [EMBL-EBI](https://www.ebi.ac.uk/training/online/course-list)
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* [UC SantaCruz Training](https://genome.ucsc.edu/training/index.html)
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* [UC Davis Workshops](http://bioinformatics.ucdavis.edu/training/documentation/)
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* [InsideDNA Tutorials](https://insidedna.me/tutorials)
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* [Stephen Turner's list](http://stephenturner.us/edu.html)
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* [Griffith's RNA-seq](https://github.com/griffithlab/rnaseq_tutorial/wiki)
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* [NCBI Tutorials](http://www.ncbi.nlm.nih.gov/home/learn.shtml)
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* [Homolog.us Tutorials](http://homolog.us/Tutorials/)
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Try searching keywords like bioinformatics, biology, genomic, genetic, data analysis, data science, computer science, life science... in these websites:
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* [Coursera](https://www.coursera.org/)
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* [edX](https://www.edx.org/)
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* [MIT](http://ocw.mit.edu/courses)
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* [eBiomics](http://ebiomics.sdcinfo.com/)
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* [Khan Academy](http://www.khanacademy.org/)
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* [Udemy](http://www.udemy.com/)
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## Coding Courses and Tutorials
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* [Code Academy](https://www.codecademy.com/#!/exercises/0)
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* [Software Carpentry](http://software-carpentry.org/lessons/)
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* [Code Snipcademy](http://code.snipcademy.com)
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* [Udacity](https://www.udacity.com/)
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* [FreeCodeCamp](https://www.freecodecamp.com/)
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* Python
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* [Matplotlib](http://www.loria.fr/~rougier/teaching/matplotlib/) - Plotting
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* [Seaborn](https://web.stanford.edu/~mwaskom/software/seaborn/tutorial.html) - Plotting
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* [Pandas](http://pandas.pydata.org/pandas-docs/stable/) - Data Analysis
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* [Machine Learning](http://scikit-learn.org/stable/documentation.html) - Library
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* [HTSeq](http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) - Library
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* R
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* [Quick-R](http://www.statmethods.net/)
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* [Swirl](http://swirlstats.com/students.html)
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* [ggplot2](http://ggplot2.org/)
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* [R & NGS](http://manuals.bioinformatics.ucr.edu/home/ht-seq#TOC-SOAP)
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* [Bioconductor Lib](http://bioconductor.org/help/workflows/)
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* [RSeek Lib Search](http://www.rseek.org/)
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* Data Analysis Pipelines
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* GNU Make
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* [Dave Tang](http://davetang.org/muse/2015/05/31/learning-about-makefiles/)
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* [Stat545](http://stat545.com/automation04_make-activity.html)
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* [ZMJones](http://zmjones.com/make/)
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* [NextFlow](http://www.nextflow.io/docs/latest/index.html)
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* [SnakeMake](http://snakemake.bitbucket.org/snakemake-tutorial.html)

‎extras/other-resources.md

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# Handy Stuff
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* [UCSC FAQ](https://genome.ucsc.edu/FAQ/)
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* Rosalind [Glossary](http://rosalind.info/glossary/)
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* [Cheatsheets](http://overapi.com/)
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* [File Format Specifications](https://github.com/samtools/hts-specs)
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* [GATK](http://gatkforums.broadinstitute.org/gatk/categories)
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* [Genome Space](https://www.broadinstitute.org/scientific-community/science/projects/genomespace/genomespace)
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* [Writing your first academic paper](https://github.com/jtleek/firstpaper)
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* [Statistics for Biologists](http://www.nature.com/collections/qghhqm)
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# Forums Q&A
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* [BioStars](https://www.biostars.org/)
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* [SEQAnswers](http://seqanswers.com/)
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* [SEQanswers - Bioinformatics](http://seqanswers.com/forums/external.php?type=RSS2&forumids=18)
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* [Bioinformatics subreddit](https://www.reddit.com/r/bioinformatics/)
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* [Bio Databases subreddit](http://www.reddit.com/r/BioDatasets)
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* [Genomic subreddit](http://www.reddit.com/r/genomics)
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* [Biology Q&A](https://biology.stackexchange.com/)
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* [Unix and GNU/Linux Q&A](https://unix.stackexchange.com/)
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* [Code Q&A](http://stackoverflow.com/)
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* [Ion Community](http://ioncommunity.lifetechnologies.com/community/)
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* [LinuxQuestions](http://www.linuxquestions.org/questions/)
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# Wikis
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* [SEQAnswers](http://seqanswers.com/wiki/SEQanswers)
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* [GNU/Linux (Arch)Wiki](https://wiki.archlinux.org/)
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# Puzzles and Code Golf
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* [Code Golf](https://codegolf.stackexchange.com/)
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* [Project Euler](https://projecteuler.net/)
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* [Rosalind](http://rosalind.info/)
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* [Hacker Rank](https://www.hackerrank.com/domains/algorithms/warmup)
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# Other lists
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* [Bioinformatics Jobs](http://www.indeed.com/q-Bioinformatics-jobs.html)
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* [Biological Databases](https://en.wikipedia.org/wiki/List_of_biological_databases) (can't be up-to-date)
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* [Genomics Papers](https://github.com/jtleek/genomicspapers) by Leek Group
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* [Bioinformatics.org Educational Services](http://www.bioinformatics.org/wiki/Educational_services)
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* [ISCB courses](http://www.iscb.org/iscb-degree-certificate-programs)
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* Learning Programming Languages [[1]](http://hackr.io/) [[2]](https://github.com/vhf/free-programming-books)
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* Software
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* [bio-tools.org](https://bio-tools.org/)
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* [CCB at JHU](http://ccb.jhu.edu/software.shtml)
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* [Galaxy Toolshed](https://toolshed.g2.bx.psu.edu/)
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* [OMICtools](http://omictools.com/about)
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* [Sanger's Isntitute list](http://www.sanger.ac.uk/science/tools)
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# Illegal resources [you should avoid](http://www.sciencemag.org/news/2016/04/whos-downloading-pirated-papers-everyone)
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* Sci-Hub
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* LibGen
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* Bookfi
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**And always, enjoy [open culture](http://www.openculture.com/)**

‎extras/paid-books.md

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# Bioinformatics - Extra Resources
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# Paid Books
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* Biological Sequence Analysis (R. Durbin et al)
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* Bioinformatics and Functional Genomics (J. Pevsner)
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* BioInfoBook [Figures](http://bioinfbook.org/php/powerpoints)
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* [Bioinformatic Algorithms](http://bioinformaticsalgorithms.com/)

‎extras/softwares.md

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# Bioinformatics - Extra Resources
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# Software Documentation
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* [Circos](http://circos.ca/documentation/course/)
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* [OpenGene Libraries](https://github.com/OpenGene)
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* [GATK Tools](https://www.broadinstitute.org/gatk/guide/tooldocs/index)
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* [ADAM](http://bdgenomics.org/) Big-Data Genomics
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* [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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* samtools 1:[BioBits'](http://biobits.org/samtools_primer.html) 2:[DaveTang's](https://github.com/davetang/learning_bam_file) 3:[YanhuiFan's](https://felixfan.github.io/bam-sam/) 4:[BinaryFlags](https://broadinstitute.github.io/picard/explain-flags.html)
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* [bcftools](https://samtools.github.io/bcftools/howtos/variant-calling.html) 1:[GATK](http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it) 2:[DaveTang's](https://github.com/davetang/learning_vcf_file) 3:[Paper](https://www.researchgate.net/publication/230658044_A_beginners_guide_to_SNP_calling_from_high-Throughput_DNA-sequencing_data)
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* bedtools 1:[Quinlan](http://quinlanlab.org/tutorials/bedtools/bedtools.html) 2:[YanhuiFan's](https://felixfan.github.io/bedtools/)
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* BWA
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* bowtie2
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* [Tuxedo Suite](http://cole-trapnell-lab.github.io/cufflinks/) 1:[YanhuiFan's](http://felixfan.github.io/tophat-cufflinks/)
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* [bedops](https://bedops.readthedocs.org/en/latest/content/usage-examples.html)
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* [picard](http://broadinstitute.github.io/picard/)
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* [jvarkit](https://github.com/lindenb/jvarkit)
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* [Exomiser](http://www.sanger.ac.uk/science/tools/exomiser) disease causing variants
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* [PopSV](https://github.com/jmonlong/PopSV) structural variants
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* [Silva](http://compbio.cs.toronto.edu/silva/) silent mutations
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* [Variant Effect Predictor](http://www.ensembl.org/info/docs/tools/vep/index.html)
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* [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/)
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* [BioGPS](http://biogps.org/help/)
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* [ABySS](http://sjackman.ca/abyss-activity/)
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* [GEMINI](https://gemini.readthedocs.io/en/latest/) annotation db
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* Graphical User Interface (GUI) apps
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* [Integrative Genomics Viewer (IGV)](https://www.broadinstitute.org/software/igv/)
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* [NCBI Genome Workbench](https://www.ncbi.nlm.nih.gov/tools/gbench/)
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* [Savant](http://genomesavant.com/p/savant/index)
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* [JBrowse](http://jbrowse.org/)
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# Other Non-specific Tools
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* [Atom](http://atom.io/) modern text editor
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* [Reference Manager](https://en.wikipedia.org/wiki/Comparison_of_reference_management_software)
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* [Git](https://git-scm.com/) Version Control
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* [HowTo Guide](https://githowto.com/)
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* [Try Online](https://try.github.io/)
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* [Pro Book](https://progit.org/)
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* [Short Videos](https://git-scm.com/videos)
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* [Start Contributing Guide](https://about.gitlab.com/2016/06/16/fearless-contribution-a-guide-for-first-timers/)
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* [LaTeX](https://latex-project.org/intro.html)
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* [Overleaf](http://www.overleaf.com/) write collaboratively
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* [Markdown](http://daringfireball.net/projects/markdown/)
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* [Here](http://markdown-here.com/)
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* RegEx [Generator](http://www.regexr.com/)
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* [Plotly](https://plot.ly/)
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* [Small (bioinformatic) Tools Manifesto](https://github.com/pjotrp/bioinformatics)
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* [Terminal Multiplexer](https://robots.thoughtbot.com/a-tmux-crash-course)
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* [ZSH](http://ohmyz.sh/)
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* [ShellCheck your scripts](http://www.shellcheck.net/)
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* Writing
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* [Correct your Grammar](https://www.grammarly.com/)
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* [Look-up word by its meaning](http://www.onelook.com/reverse-dictionary.shtml)
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* google translate, obviusly.
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* [Introduction to HTML](https://developer.mozilla.org/en-US/docs/Web/Guide/HTML/Introduction)

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