Final grades and appeals | |
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Dear students, We have published the final grades. Those who submitted their project on time will be able to access the feedbacks on the GR website. Otherwise, please send me an email and I will provide feedback manually. Please note that we will only consider appeals accompanied by a justification as to why and where an amendment to the grade should be considered. Please take this seriously and keep in mind that an appeal and re-examination of the work may result in a downgrade. Best, Almog |
| פורסם ב-10/4/2022, 19:26:46 Created on 10/4/2022, 19:26:46 Создано10/4/2022, 19:26:46 تم النشر ب-10/4/2022, 19:26:46 |
Final project submission deadline extended | |
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Dear students, We are extending the deadline for submitting the final project by one week. The new deadline is 27/03/2021. Best, Almog |
| פורסם ב-14/3/2022, 09:48:55 Created on 14/3/2022, 09:48:55 Создано14/3/2022, 09:48:55 تم النشر ب-14/3/2022, 09:48:55 |
Workflow submission deadline | |
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Dear students, Please note that the deadline for workflow submission is 28/02 (next Monday). Late submission will affect your final grade! Remember: - Look for RNA-seq data only (bulk or single-cell)! - Look for the raw count matrix (you can use normalized count matrix, but without DESeq2 - use limma instead). - For each dataset describe the groups and the samples. - Workflow should be sent to ualmog.angelatcampus.technion.ac.il as a PDF named ID1_ID2.pdf. Best, Almog |
| עדכון אחרון ב-24/2/2022, 12:08:09 Last updated on 24/2/2022, 12:08:09 Последняя модификация24/2/2022, 12:08:09 تمت الحتلنة الأخيرة ب-24/2/2022, 12:08:09 |
(!) Clarifications regarding using normalized data for the final project (!) | |
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Dear students, Many of you have asked me if normalized (TPM, FPKM, etc.) counts data can be used with DESeq2. The answer is no, DESeq2 has to get unnormalized counts data as an input. If you only have access to normalized data and you want to perform a differential expression analysis you can use the package limma* instead of DESeq2. Otherwise, please find other data. * There are many excellent tutorials/vignettes available for limma (use Google/YouTube). Good luck, Almog |
| פורסם ב-20/2/2022, 10:13:09 Created on 20/2/2022, 10:13:09 Создано20/2/2022, 10:13:09 تم النشر ب-20/2/2022, 10:13:09 |
The lecture and tutorial will take place via Zoom | |
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Dear students, Please note that the rest of this course will be held only via Zoom. Best, Dvir and Almog |
| פורסם ב-17/1/2022, 08:28:07 Created on 17/1/2022, 08:28:07 Создано17/1/2022, 08:28:07 تم النشر ب-17/1/2022, 08:28:07 |
Thursday's tutorial and reception hour (13/1/22) | |
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Dear students, The tutorial today will take place only via Zoom. Additionally, students who wish to discuss HW4 are welcome to stay in the session - I will be available until 13:30. Best, Almog |
| פורסם ב-13/1/2022, 08:23:01 Created on 13/1/2022, 08:23:01 Создано13/1/2022, 08:23:01 تم النشر ب-13/1/2022, 08:23:01 |
Clarifications and questions regarding HW4 | |
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Dear students, First, please note that one of the sections in question 4 under "results" has a problem: Instead of - "In the METABRIC dataset, there is no significant difference in overall survival of BC-ImH is significantly lower than BC-ImL." the question should be - "In the METABRIC dataset, there is no significant difference in overall survival between BC-ImH and BC-ImL." Additionally, you are highly recommended to attend the reception hour after Thursday's tutorials if you have questions or need clarifications. I will be available following the tutorial for an hour on the same Zoom link. Please keep in mind that sending questions via e-mail might take me 2-3 days to reply, and I won't be able to assist once the submission is due. Best, Almog |
| פורסם ב-11/1/2022, 10:38:32 Created on 11/1/2022, 10:38:32 Создано11/1/2022, 10:38:32 تم النشر ب-11/1/2022, 10:38:32 |
The lecture and tutorial will take place via Zoom tomorrow (10/01/22) | |
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Dear students, The lecture and tutorial following it will be conducted via Zoom. Best, Dvir and Almog |
| פורסם ב-9/1/2022, 18:07:29 Created on 9/1/2022, 18:07:29 Создано9/1/2022, 18:07:29 تم النشر ب-9/1/2022, 18:07:29 |
HW4 is published | |
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Dear students, HW4 is published, the due date is 20/1/22. Best, Almog |
| פורסם ב-6/1/2022, 12:47:55 Created on 6/1/2022, 12:47:55 Создано6/1/2022, 12:47:55 تم النشر ب-6/1/2022, 12:47:55 |
Thursday's tutorial and reception hour (6/1/22) | |
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Dear students, The tutorial tomorrow will take place only via Zoom. Additionally, students who wish to discuss HW3 are welcome to stay in the session - I will be available until 13:30. Best, Almog |
| פורסם ב-5/1/2022, 11:55:21 Created on 5/1/2022, 11:55:21 Создано5/1/2022, 11:55:21 تم النشر ب-5/1/2022, 11:55:21 |
Requirements for tomorrow's tutorial (10) | |
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Dear students, The tutorial tomorrow will focus on single-cell RNA sequencing (scRNA-seq) analysis. To be prepared, please read and follow these instructions in advance: (1) Install those packages from CRAN/Bioconductor: Seurat, SingleR, celldex, Matrix, ggplot2, ggtree, SingleCellExperiment, scDblFinder and dittoSeq (2) Download 10X Non-Small Cell Lung Cancer data: - Go to: https://support.10xgenomics.com/single-cell-vdj/datasets/2.2.0/vdj_v1_hs_nsclc_5gex - Sign in and download "Gene / cell matrix (filtered)" - Unzip Best, Almog |
| פורסם ב-2/1/2022, 14:36:32 Created on 2/1/2022, 14:36:32 Создано2/1/2022, 14:36:32 تم النشر ب-2/1/2022, 14:36:32 |
HW3 clarification | |
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Dear students, There is a minor mistake in the first section of "Make a boxplot of Fructosamine concentrations for different alleles in Belgian and German Shepherds". You don't need to use the genotype data of Labrador Retriever. Namely, only data from Belgian and German Shepherds. Best, Almog |
| פורסם ב-2/1/2022, 09:30:33 Created on 2/1/2022, 09:30:33 Создано2/1/2022, 09:30:33 تم النشر ب-2/1/2022, 09:30:33 |
Thursday's tutorial | |
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Dear students, The tutorial tomorrow (30/12) will take place only via Zoom. Best, Almog |
| פורסם ב-29/12/2021, 09:55:02 Created on 29/12/2021, 09:55:02 Создано29/12/2021, 09:55:02 تم النشر ب-29/12/2021, 09:55:02 |
HW3 is published | |
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Dear students, HW3 is published, the due date is 6/1/22. Best, Almog |
| פורסם ב-23/12/2021, 21:40:54 Created on 23/12/2021, 21:40:54 Создано23/12/2021, 21:40:54 تم النشر ب-23/12/2021, 21:40:54 |
HW3 and HW4 start and due dates | |
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Dear students, The start and due dates of HW3 and HW4 have been postponed by a week. Attached here is the updated timetable: 16/12/21 HW2-Due 23/12/21 HW3-Start 06/01/22 HW3-Due, HW4-Start 20/01/22 HW4-Due, FP-Start Best, Almog |
| פורסם ב-13/12/2021, 13:50:42 Created on 13/12/2021, 13:50:42 Создано13/12/2021, 13:50:42 تم النشر ب-13/12/2021, 13:50:42 |
HW2 - submission | |
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Dear students, Please note that HW2 submission should be in a .ZIP file Best, Almog |
| פורסם ב-5/12/2021, 11:50:53 Created on 5/12/2021, 11:50:53 Создано5/12/2021, 11:50:53 تم النشر ب-5/12/2021, 11:50:53 |
HW2 is published | |
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Dear students, HW2 is published, the due date is 16/12. Best, Almog |
| פורסם ב-2/12/2021, 21:41:47 Created on 2/12/2021, 21:41:47 Создано2/12/2021, 21:41:47 تم النشر ب-2/12/2021, 21:41:47 |
Timetable for homework assignments | |
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Dear Students, Here are some announcements regarding HW assignments: 1. Please note that HW1 is due tomorrow (25/11) 2. Due dates and start dates for HW2-4: - 25/11/21 - HW1 - due date - 02/12/21 - HW2 - start date (Hannuka no class) - 16/12/21 - HW2 - due date, HW3 - start date - 30/12/21 - HW3 - due date, HW4 - start date - 13/01/22 - HW4 - due date - 20/01/22 - Final Project - start date (due date will be announced later on) 3. Considering the tight timetable, HW2-4 will be shorter than HW1 Good luck, Almog |
| פורסם ב-24/11/2021, 13:45:03 Created on 24/11/2021, 13:45:03 Создано24/11/2021, 13:45:03 تم النشر ب-24/11/2021, 13:45:03 |
HW1 clarifications | |
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Dear students, Please read the following clarifications regarding HW1: - I am aware that there is inconsistency with "covid_deaths" and "covid.deaths". It doesn't matter which one you choose, just stick to it throughout the analysis. - Regarding the question: "Do you agree with the claim that increased human development index causes increase in COVID-19 mortality (write in detail)?" You need to decide, based on the correlation analysis, whether this is enough evidence to say that the increase in the human development index causes an increase in COVID-19 mortality. If not, why? you can also find an alternative explanation (the bonus question). Good luck, Almog |
| פורסם ב-16/11/2021, 17:11:54 Created on 16/11/2021, 17:11:54 Создано16/11/2021, 17:11:54 تم النشر ب-16/11/2021, 17:11:54 |
Required packages and data for tutorial 4 | |
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Dear students, Tomorrow we will be analyzing RNA-Seq data with the package "DESeq2". I highly recommend downloading and installing all the necessary packages in advance. You can find a Rmarkdown file on the course website with all the necessary packages. Note that you need to install Bioconductor for some of them. Best, Almog |
| פורסם ב-14/11/2021, 18:57:39 Created on 14/11/2021, 18:57:39 Создано14/11/2021, 18:57:39 تم النشر ب-14/11/2021, 18:57:39 |
Tutorial 3 cancelation (Thursday 11/11/2021) | |
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Dear student, Unfortunately, I will not be able to teach today's tutorial in the classroom. The tutorial recording and homework assignment will be uploaded to the course website later in the day. Best, Almog |
| פורסם ב-11/11/2021, 07:26:43 Created on 11/11/2021, 07:26:43 Создано11/11/2021, 07:26:43 تم النشر ب-11/11/2021, 07:26:43 |
Required packages for tutorial 3 and tutorials 1 and 2 recordings | |
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Dear students, 1. In order to save time for Thursday's tutorial, please go to the Tutorial 3 directory under the course material and download an R markdown file called "Bioconductor packages to install". Once you open the file in R install all the packages (both from Bioconductor and CRAN). In addition, go to the directory "FASTA file" and save those files under the same directory on your computer. 2. Tutorials 1 and 2 recordings are now available on YouTube. Best, Almog |
| פורסם ב-8/11/2021, 19:45:12 Created on 8/11/2021, 19:45:12 Создано8/11/2021, 19:45:12 تم النشر ب-8/11/2021, 19:45:12 |
Tutorial 1 recording | |
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Due to technical issues, I did not manage to record our last tutorial in the class. I will record another video and it will be available this week. Apologize for the delay, Almog |
| פורסם ב-30/10/2021, 19:34:16 Created on 30/10/2021, 19:34:16 Создано30/10/2021, 19:34:16 تم النشر ب-30/10/2021, 19:34:16 |
Required software for the tutorials and some recommendations | |
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Dear students, In our upcoming tutorials, you will be working with biological data and for this purpose, we will use R. R is a popular programming language among data scientists and bioinformaticians. Before our first tutorial please make sure you do this: 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 C/C++. 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 tidyverse collection of packages that include most of the packages that 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 in the tidyverse 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 during the tutorial I will give you some tasks to try and write code by yourself. 3. Please fill up the questionnaire, spare a few minutes to tell us about yourself and your expectations. It helps us make the course and the tutorial better. https://forms.gle/2azYeRN5hK6Yq7HD8 Feel free to e-mail if you need any help - ualmog.angelatcampus.technion.ac.il Best, Almog |
| עדכון אחרון ב-21/10/2021, 13:59:35 Last updated on 21/10/2021, 13:59:35 Последняя модификация21/10/2021, 13:59:35 تمت الحتلنة الأخيرة ب-21/10/2021, 13:59:35 |
We want to get to know you | |
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It's 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/2azYeRN5hK6Yq7HD8 It will help us understand who you are, what is your background, and what you hope to gain from this course. Best, Dvir & Almog |
| פורסם ב-17/10/2021, 15:14:25 Created on 17/10/2021, 15:14:25 Создано17/10/2021, 15:14:25 تم النشر ب-17/10/2021, 15:14:25 |