.. Foundations in Computational Skills documentation master file, created by sphinx-quickstart on Mon Jul 10 16:33:38 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to Foundations in Computational Skills's documentation! =============================================================== .. toctree:: :hidden: :maxdepth: 1 :caption: Contents: Workshop 0 - CLI Workshop 1 - python Workshop 2 - NGS 1 Workshop 3 - Advanced CLI Workshop 4 - Introduction to R Workshop 5 - NGS 2 Workshop 6 - Cluster Computing Contents -------- - `Workshop 0 - CLI Basics`_ - `Workshop 1 - python`_ - `Workshop 2 - High throughput sequencing application`_ - `Workshop 3 - Advanced CLI`_ - `Workshop 4 - Introduction to R`_ - `Workshop 5 - High throughput sequencing application part 2`_ - `Workshop 6 - Shell scripting and cluster computing`_ Friendly Introduction --------------------- .. youtube:: OQzcX019Vmc List of topics -------------- .. note:: These workshops are still under construction Please be kind. Workshop 0 - CLI Basics +++++++++++++++++++++++ :doc:`content/workshops/00_cli_basics/00_cli_basics` ======================================== ======= Topic Length ======================================== ======= `CLI Introduction`_ 3 min `Navigating directories, listing files`_ 16 min `Basic file operations`_ 9 min `Working with files 1`_ 10 min `Working with files 2`_ 10 min `I/O redirection and related commands`_ 20 min `Globbing`_ 6 min ======================================== ======= .. _`CLI Introduction`: http://www.youtube.com/watch?v=M5I6pNxVln4 .. _`Navigating directories, listing files`: https://www.youtube.com/watch?v=MmHcOPJEjGA .. _`Basic file operations`: https://www.youtube.com/watch?v=qG8qn4ZARvg .. _`Working with files 1`: https://www.youtube.com/watch?v=hNb8gIHvN04 .. _`Working with files 2`: https://www.youtube.com/watch?v=MJI4xTuxdPg .. _`I/O redirection and related commands`: https://www.youtube.com/watch?v=WXcvQ5F7Kh4 .. _`Globbing`: https://www.youtube.com/watch?v=6iQEKElUoI8 Workshop 1 - python +++++++++++++++++++ :doc:`content/workshops/01_python/01_python_script` :doc:`content/workshops/01_python/01_python_workshop` ======================================================== ======= Topic Length ======================================================== ======= Introduction 3 min Builtin Types 2 min A Simple Program 6 min if Statements 3 min Simplifying Solution 4 min Defining Functions 4 min More On Types and Iteration 4 min More Data Structures - File I/O 22 min Modules 3 min Executing Scripts with Arguments from the Command Line 3 min Other File objects - ======================================================== ======= Workshop 2 - High throughput sequencing application +++++++++++++++++++++++++++++++++++++++++++++++++++ :doc:`content/workshops/02_seq_process_app/02_seq_process_app` :doc:`content/workshops/02_seq_process_app/02_seq_process_app_workshop` ========================================= ======= Topic Length ========================================= ======= `App Session Introduction`_ 2 min `Illumina Sequencing Technology`_ 5 min `High Throughput Sequencing Data Primer`_ 9 min `Sequencing Data QC and Analysis Primer`_ 9 min ========================================= ======= .. _`App Session Introduction`: http://www.youtube.com/watch?v=67odXeyn27M .. _`Illumina Sequencing Technology`: https://www.youtube.com/watch?v=fCd6B5HRaZ8 .. _`High Throughput Sequencing Data Primer`: http://www.youtube.com/watch?v=WLnYTiHwWAA .. _`Sequencing Data QC and Analysis Primer`: http://www.youtube.com Workshop 3 - Advanced CLI +++++++++++++++++++++++++ :doc:`content/workshops/03_advanced_cli/03_advanced_cli` :doc:`content/workshops/03_advanced_cli/03_advanced_cli_workshop` ========================================= ============== Topic Length ========================================= ============== `nano`_ ~7 min vim (part `one`_, `two`_, `three`_) ~9, ~6, ~6 min `emacs`_ ~24 min `piping, silencing stdout/stderr`_ ~10 min `shell tricks`_ ~10 min `bash history`_ ~4 min `pushd/popd, find, xargs/fim`_ ~10 min ========================================= ============== .. _nano: http://www.youtube.com/watch?v=cLyUZAabf40 .. _one: http://www.youtube.com/watch?v=c6WCm6z5msk .. _two: http://www.youtube.com/watch?v=BPDoI7gflxM .. _three: http://www.youtube.com/watch?v=J1_CfIb-3X4 .. _emacs: http://www.youtube.com/watch?v=16Rd46SE-20 .. _piping, silencing stdout/stderr: http://www.youtube.com/watch?v=vLJOmO1WYL4 .. _shell tricks: http://www.youtube.com/watch?v=7lSdSbgvAvs .. _bash history: http://www.youtube.com/watch?v=WG-MGFPsLhk .. _pushd/popd, find, xargs/fim: http://www.youtube.com/watch?v=k_Qt2khwA7c Workshop 4 - Introduction to R ++++++++++++++++++++++++++++++++++++ :doc:`content/workshops/04_R/04_R` :doc:`content/workshops/04_R/R_04_workshop` ========================================= ============== Topic Length ========================================= ============== `Reasons why you should learn R`_ ~7 min `RStudio interface`_ ~10 min `Installing packages`_ ~7 min `Console and working environment basics`_ ~8 min `Very quick data types`_ ~7 min `NAs, NaNs, Infs`_ ~3 min `Intro to vectors`_ ~7 min `Data types and structures, Part 2`_ 9:30 min `If statements and logical operators`_ 5:30 min `Apply function`_ ~7 min `Reshape package`_ ~6 min `Split, Apply and Combine with plyr`_ 8:30 min `Intro to ggplot`_ 9 min ========================================= ============== .. _Reasons why you should learn R: http://www.youtube.com/watch?v=G1PLkaRL2iY .. _RStudio interface: http://www.youtube.com/watch?v=jAgbZ8jkBtQ .. _Installing packages: http://www.youtube.com/watch?v=0cCuHhfphtQ .. _Console and working environment basics: http://www.youtube.com/watch?v=v5g_JZK_Ggs .. _Very quick data types: http://www.youtube.com/watch?v=B2f9tSGVn7w .. _NAs, NaNs, Infs: http://www.youtube.com/watch?v=ofe2hDUg78g .. _Intro to vectors: http://www.youtube.com/watch?v=uUxwf1lWgrk .. _Data types and structures, Part 2: http://www.youtube.com/watch?v=_HKDbA9WkX8 .. _If statements and logical operators: http://www.youtube.com/watch?v=eVEx_pBEkRI .. _Apply function: http://www.youtube.com/watch?v=csLati8vpOo .. _Reshape package: http://www.youtube.com/watch?v=aXXy04P_l1c .. _Split, Apply and Combine with plyr: http://www.youtube.com/watch?v=S4oCN0FDC14 .. _Intro to ggplot: http://www.youtube.com/watch?v=O9tudYwK1RM Workshop 5 - High throughput sequencing application part 2 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ :doc:`content/workshops/05_ngs_app_session_2/05_ngs_app_session_2` :doc:`content/workshops/05_ngs_app_session_2/05_ngs_app_session_2_workshop` There are no video online materials for this workshop. Workshop 6 - Shell scripting and cluster computing ++++++++++++++++++++++++++++++++++++++++++++++++++ :doc:`content/workshops/06_cluster_computing/06_cluster_computing` ------------ Contributors ------------ The primary contributors to the BU Bioinformatics Programming Workshop Taskforce: - Gracia Bonilla - Rachael Ivison - Vinay Kartha - Josh Klein - Adam Labadorf - Katharine Norwood We would also like to thank Gary Benson for his mentorship and support. Indices and tables ------------------ * :ref:`genindex` * :ref:`modindex` * :ref:`search`