Presentations day 23/3 new location | |
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Dear student, Please note that the location has changed to Taub 8. Best, Almog |
| פורסם ב-22/3/2023, 12:26:57 Created on 22/3/2023, 12:26:57 Создано22/3/2023, 12:26:57 تم النشر ب-22/3/2023, 12:26:57 |
Presentations day | |
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Dear students, Presentation days are nearby! 1. Make sure you are on the list - https://docs.google.com/spreadsheets/d/12b0DXewil3QvEn7st6D9Z4Tb6n7ILmGIRqzbsUgFAC8/edit?usp=sharing 2. All students registered for a session should be in class before it begins (9 AM, 10 AM, 11 AM...) 3. Be at Taub 6 10 minutes before your session begin. 4. Send your presentation to Almog no late than 8:00 in the morning of your presentation day! I wish you all the best, Almog |
| פורסם ב-19/3/2023, 09:54:39 Created on 19/3/2023, 09:54:39 Создано19/3/2023, 09:54:39 تم النشر ب-19/3/2023, 09:54:39 |
The final project submission date changed to 20/3 | |
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Dear students, Please note that the submission due date has changed to 20/3. Good luck, Almog |
| פורסם ב-8/3/2023, 18:07:10 Created on 8/3/2023, 18:07:10 Создано8/3/2023, 18:07:10 تم النشر ب-8/3/2023, 18:07:10 |
Final project forum and tutorial 12 recording | |
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Dear student, Congratulations! you have reached the last assignment for this course. Below are some notifications regarding the final project and the last tutorial: - Tutorial 12 (microbiome data analysis) recording and presentation are now available in the course material. - I opened a forum for the final project, you can join with the following link: https://piazza.com/technion.ac.il/winter2023/236523 - Use the forum to ask questions, find partners, and share tips with your classmates about the final project. Last but not least, if you like bioinformatics and wish to learn more, you can talk with me anytime, I would be happy to share more information. Wish you all good luck., Almog |
| עדכון אחרון ב-29/1/2023, 14:53:17 Last updated on 29/1/2023, 14:53:17 Последняя модификация29/1/2023, 14:53:17 تمت الحتلنة الأخيرة ب-29/1/2023, 14:53:17 |
Cancellation of tomorrow and next Monday tutorials | |
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Dear students, We will not have a tutorial tomorrow (18/1) or Monday (23/1). Instead, I will upload a recording of "microbiome data analysis and random forest". In addition, in the last tutorial (26/1) I will discuss the final project and give you general instructions, tips, and more. Don't worry if you can't be there on Thursday, I will also send the recording. Best, Almog |
| פורסם ב-18/1/2023, 12:10:50 Created on 18/1/2023, 12:10:50 Создано18/1/2023, 12:10:50 تم النشر ب-18/1/2023, 12:10:50 |
HW4 is published | |
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Dear students, HW4 has been published, and it is due on January 26. Best, Almog |
| פורסם ב-12/1/2023, 10:16:17 Created on 12/1/2023, 10:16:17 Создано12/1/2023, 10:16:17 تم النشر ب-12/1/2023, 10:16:17 |
HW3 due date extension | |
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Dear student, The submission deadline for HW3 has been extended by two days. Best, Almog |
| פורסם ב-9/1/2023, 17:14:32 Created on 9/1/2023, 17:14:32 Создано9/1/2023, 17:14:32 تم النشر ب-9/1/2023, 17:14:32 |
Few announcements regarding the next homework assignment and midterm exam | |
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Due to schedule restrictions, there are a few changes: 1. We have postponed HW3 start date until after Hanukkah on Monday (26/12). This assignment will focus on cancer analysis using the TCGA database. 2. For now there will be no midterm exam. 3. The final homework assignment (and also HW3 due) will be on Monday (9/1) and will be dealing with genome-wide association studies (GWAS) and single-cell RNA-Seq analysis. Happy holiday, Almog |
| פורסם ב-15/12/2022, 21:22:48 Created on 15/12/2022, 21:22:48 Создано15/12/2022, 21:22:48 تم النشر ب-15/12/2022, 21:22:48 |
Important correction for HW2 | |
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Dear students, There is a mistake when writing HW2, please note: While screening many datasets to write this homework, I mistakenly skipped the step where you check that the order of the samples in the metadata and count matrix match. As a result, the volcano plot (after the correction for Subjects) would still not result in any significant genes. For the sake of this HW please skip the step when you check that the samples in the metadata correspond to the columns in counts. For example: counts <- counts[,metadata$Sample] This should result in some significant genes in the second volcano plot for the GSEA questions. If you already submitted the homework, don't worry we will take this into account when checking. I apologize for the mistake, always remember to check that your metadata and counts tables match :) Best, Almog |
| פורסם ב-9/12/2022, 12:41:26 Created on 9/12/2022, 12:41:26 Создано9/12/2022, 12:41:26 تم النشر ب-9/12/2022, 12:41:26 |
Tutorials 5 and 6 recording | |
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Dear students, Unfortunately, there is a problem with tutorial 5 video (screen recording stopped). Attached here is last year's tutorial and some good videos on YouTube (there are plenty more): https://www.youtube.com/watch?v=-HvXQRU_1sI https://www.youtube.com/watch?v=0b24mpzM_5M https://www.youtube.com/watch?v=OzNzO8qwwp0 * Please note that the code changed from last year Best, Almog |
| עדכון אחרון ב-5/12/2022, 17:40:39 Last updated on 5/12/2022, 17:40:39 Последняя модификация5/12/2022, 17:40:39 تمت الحتلنة الأخيرة ب-5/12/2022, 17:40:39 |
Computational & Cancer Genomics Conference | |
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Hi, I mentioned in class this upcoming conference: https://ccg2022.net.technion.ac.il/ There is a registration fee of 300 NIS (that includes lunch), but we will allow students to join the sessions freely (without lunch). Best, Dvir |
| פורסם ב-30/11/2022, 15:17:54 Created on 30/11/2022, 15:17:54 Создано30/11/2022, 15:17:54 تم النشر ب-30/11/2022, 15:17:54 |
HW2 is published | |
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Dear students, HW2 has been published, and it is due on December 12. Best, Almog |
| עדכון אחרון ב-28/11/2022, 22:15:01 Last updated on 28/11/2022, 22:15:01 Последняя модификация28/11/2022, 22:15:01 تمت الحتلنة الأخيرة ب-28/11/2022, 22:15:01 |
Tutorial 4 recording | |
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Dear students, Attached here is a recording of tutorial 4: https://www.youtube.com/watch?v=X57CdcEx_ec Best, Almog |
| פורסם ב-21/11/2022, 13:29:25 Created on 21/11/2022, 13:29:25 Создано21/11/2022, 13:29:25 تم النشر ب-21/11/2022, 13:29:25 |
Apologize for the tutorial 4 cancelation | |
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Dear students, I got confused with today's tutorial hours. Apologize for not being there on time. I highly recommend coming to Monday's tutorial. In addition, I will schedule a meeting in Zoom for those who can't be there and share the recording. Please send me an e-mail if you are interested. Best, Almog |
| פורסם ב-17/11/2022, 14:48:13 Created on 17/11/2022, 14:48:13 Создано17/11/2022, 14:48:13 تم النشر ب-17/11/2022, 14:48:13 |
HW1 is published | |
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Dear students, HW1 has been published, and it is due on November 28. Best, Almog |
| פורסם ב-14/11/2022, 21:28:15 Created on 14/11/2022, 21:28:15 Создано14/11/2022, 21:28:15 تم النشر ب-14/11/2022, 21:28:15 |
Tutorial 3 requirements | |
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Dear students, In our next tutorial, we will practice sequence alignment in R. Therefore, I highly recommend bringing laptops. To save time, please download "tutorial_3.zip" from the course website and open the file "tutorial3_packages.Rmd". You will need to install the Bioconductor package manager in order to install some of the packages that are required for the class exercise. In addition, the first homework assignment will be released on Monday. My apologies for any confusion caused. Best, Almog |
| פורסם ב-9/11/2022, 14:47:55 Created on 9/11/2022, 14:47:55 Создано9/11/2022, 14:47:55 تم النشر ب-9/11/2022, 14:47:55 |
Mid-term exam | |
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Hi, 1. There will be no zoom or recordings this year. 2. The mid-term exam will be during the Wednesday class of December 28th, 2022. As explained, you do not need to learn for this exam, it will be questions about what we learned. Have a great semester! Dvir |
| פורסם ב-26/10/2022, 13:29:17 Created on 26/10/2022, 13:29:17 Создано26/10/2022, 13:29:17 تم النشر ب-26/10/2022, 13:29:17 |
Requirements for the tutorials and some recommendations | |
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Dear students, In our upcoming tutorials, you will analyze different types of biological data and for this purpose, we will use R. R is a popular programming language among, statisticians, data scientists and bioinformaticians. Do the following before our first tutorial: 1. Install R and Rstudio (a user-friendly IDE for R) by following the instructions below: https://rstudio-education.github.io/hopr/starting.html 2. Packages installation: R packages are similar to libraries in Python. Please take a few minutes to understand the concept of packages as described at: https://rstudio-education.github.io/hopr/packages2.html For our first lessons, you’ll need to install the tidyverse package collection, which includes many of the packages you’re likely to use in data analyses (such as ggplot2, dplyr, stringr etc.). Install all the packages in the tidyverse by running - install.packages("tidyverse") command in the Rstudio console window. You can read about different packages here: https://www.tidyverse.org/packages/ Recommendations: 1. In our first tutorial we will get familiar with R and Rstudio, however, this is just a drop in the ocean. I encourage you to learn the basic syntax of R before our first tutorial. There are endless introduction videos for R on youtube - I am sure you will find the one that is best for you. 2. Bring your laptop for the tutorials. you don't have to, but it is recommended since I will give you some tasks to try and write code by yourself during the tutorial. 3. Please fill up the questionnaire, and spare a few minutes to tell us about yourself. It helps us make the course and the tutorial better. https://forms.gle/o97XUEMwC51NmfKX9 Feel free to e-mail if you need any help - ualmog.angelatcampus.technion.ac.il Best, Almog |
| עדכון אחרון ב-25/10/2022, 21:54:11 Last updated on 25/10/2022, 21:54:11 Последняя модификация25/10/2022, 21:54:11 تمت الحتلنة الأخيرة ب-25/10/2022, 21:54:11 |
24/10 Monday's tutorial | |
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Dear students, Please notice that there will be NO tutorial this Monday (24/10). Our first tutorial will be on Thursday (27/10). Every tutorial on Mondays will be identical to the previous one on Thursdays. Best, Almog |
| פורסם ב-18/10/2022, 12:32:48 Created on 18/10/2022, 12:32:48 Создано18/10/2022, 12:32:48 تم النشر ب-18/10/2022, 12:32:48 |
We want to get to know you | |
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It's only a week until the start of the semester, and we are excited to get to know you. Please fill out the following questionnaire: https://forms.gle/o97XUEMwC51NmfKX9 It will help us understand who you are, what is your background, and what you hope to gain from this course. Best, Dvir Aran Almog Angel |
| פורסם ב-18/10/2022, 08:59:39 Created on 18/10/2022, 08:59:39 Создано18/10/2022, 08:59:39 تم النشر ب-18/10/2022, 08:59:39 |