PROGRAM EN CIENCIAS BIOLÓGICAS - P2269-TEÓRICO-PRACTICO-N0026-06-N01

Clase 1

• Biolinux® (Biolinux for Scientists, 2014). Biolinux for Scientists. https://www.bioinformatics.org/groups/?group_id=341
• Lubuntu 20.04 (Lubuntu Development Team, 2020). Lubuntu 20.04. https://lubuntu.me/focal-released/
• LXDE (LXDE Project, 2024). LXDE. https://www.lxde.org/
• Oracle VirtualBox® (Oracle Corporation, 2024). Oracle VirtualBox®. https://www.virtualbox.org/
• GNU Bash Project (Free Software Foundation, 2024). GNU Bash Project. https://www.gnu.org/software/bash/
• Python (Python Software Foundation, 2024). Python. https://www.python.org/
• The R Project for Statistical Computing (R Development Core Team, 2024). The R Project for Statistical Computing. https://www.r-project.org/

Clase 2

• Función GNU. (2024). General introduction to AWK®. Recuperado de https://www.gnu.org/software/gawk/manual/gawk.html
• Linux man pages. (s.f.). awk(1p) — Linux manual page. Recuperado de https://man7.org/linux/man-pages/man1/awk.1p.html
• Li, H. (s.f.). Proyecto bioawk®. Recuperado de https://github.com/lh3/bioawk
• TutorialsPoint. (2021). Bash scripting tutorial. Recuperado de https://www.tutorialspoint.com/unix/unix-shell.htm

Clase 3

• Fundación GNU. (2024). Bash Reference Manual. Recuperado de https://www.gnu.org/software/bash/manual/bash.html
• The Linux Documentation Project. (2014). Advanced Bash-Scripting Guide: An in-depth exploration of the art of scripting. Recuperado de https://tldp.org/LDP/abs/html/
• Fundación GNU. (2024). sed, a stream editor. Recuperado de https://www.gnu.org/software/sed/manual/sed.html
• Babraham Bioinformatics Institute. (2024). FastQC: A quality control tool for high throughput sequence data. Recuperado de https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Clase 4

• Shenwei, S. (2024). SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. Recuperado de https://github.com/shenwei356/seqkit?tab=readme-ov-file
• Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. iMeta, e191. https://doi.org/10.1002/imt2.191
• IBM. (2023). crontab Command. Recuperado de https://www.ibm.com/docs/hr/aix/7.1?topic=c-crontab-command

Clase 5

• Paradis, E. (2003). R para principiantes. Institut des Sciences de l’Evolution, Université Montpellier II. Disponible en https://cran.r-project.org/doc/contrib/rdebuts_es.pdf
• R Development Core Team. (2000). Introducción a R. Disponible en https://cran.r-project.org/doc/contrib/R-intro-1.1.0-espanol.1.pdf
• Beasley, C. R. (2004). Bioestatística Usando R. Disponible en https://cran.r-project.org/doc/contrib/Beasley-BioestatisticaUsandoR.pdf

Clase 6

• Andrews, H., & Herzberg, A. (1988). The Iris data set: Data book. UCI Machine Learning Repository. Disponible en https://archive.ics.uci.edu/dataset/53/iris
• Santana, J., & Farfán, E. (2014). El arte de programar en R: un lenguaje para la estadística. Disponible en https://cran.r-project.org/doc/contrib/Santana_El_arte_de_programar_en_R.pdf
• Wikibooks contributors. (2024). Non-Programmer’s Tutorial for Python 3. En Wikibooks. Disponible en https://upload.wikimedia.org/wikipedia/commons/1/1d/Non-Programmer%27s_Tutorial_for_Python_3.pdf
• Bassi, S. (2018). Python for bioinformatics (Second Edition). Disponible en http://englishonlineclub.com/pdf/Python%20for%20Bioinformatics%20(Second%20Edition)%20[EnglishOnlineClub.com].pdf
• Severance, R. (2020). Python para todos, Explorando la información con Python 3. Disponible en https://do1.dr-chuck.com/pythonlearn/ES_es/pythonlearn.pdf

Clase 7

• Biopython. (2025). Biopython: Python tools for computational molecular biology. Recuperado de https://biopython.org/
• Bassi, S. (2018). Python for bioinformatics (2ª ed.). Recuperado de http://englishonlineclub.com/pdf/Python%20for%20Bioinformatics%20(Second%20Edition)%20[EnglishOnlineClub.com].pdf

Clase 8

• Himes et al. (2014). RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells. PLoS One. Recuperado el [Insert Date of Retrieval] de https://bioconductor.org/packages/release/data/experiment/manuals/airway/man/airway.pdf
• Chang, J., Chapman, B., Friedberg, I., Hamelryck, T., de Hoon, M., Cock, P., ... & Wilczyński, B. (2021). Biopython Tutorial and Cookbook. [Add retrieval information if it's an online resource with a specific URL]