marskar / biof309_fall2018 Goto Github PK

I am trying to upload my files to a new GitHub repo (or an old one, I don't really care). All of my online searching through JetBrains documentation says to click on the "Local Changes" tab, then commit and push" but I do not have that "Local Changes" tab available to me.

I expect that the "Local Changes" tab is only present if you initially opened the project from a pre-made GitHub repo with intent to edit the files then push them back. I, however, started the project on my computer, and now want to upload all my files to a repo on GitHub. Do you have any quick advice? I know we did this in an early class I could probably just go back and watch that again.

I am able to "commit" the files by pressing a green check mark at the top right of my PyCharm screen, but do not know how to push them.

I have tried this tutorial "https://help.github.com/articles/adding-an-existing-project-to-github-using-the-command-line/" in the terminal in PyCharm with little avail. Any suggestions.

I don't know how to open the slide.html file as slides in github.

#1. Downloading the datasets

Once you arrived at the site, you are going to search for the things that you would like to study. For instance, you can write in the search breast cancer and all the data available that used breast cancer will show up.

As an example I will be using three datasets of RNA-seq expression of lung epithelial and mesenchymal cells at different embryonic stage:

*GSM2319567 (lung 9.5 embryo expression)

*GSM3027039 (lung 10.5 embryo expression)

*GSM3027047 (lung 11.5 embryo expression)

To download the data you can go to end and dowload the series matrix. GSE files are the one that contain the data to be analyzed and GPL files contain the annotation. When working with your own questions I recommend downloading both to help you know what mRNA data you are analyzing.

I am going to include the steps to download one of the datasets and save this data to help you find the data when the files are added as a supplement information instead of a series matrix.

-Look on this data on the search bar

-In the bottom of the pages sometimes are instruction that will help you find the data. As you see in the instruction "Raw data are available in SRA"

-Now, find your dataset!

-Downloading the datasets

-Final step

You have your data. Now what?

-You need to filter the data either in Excel or python to facilitates its use.

I am in my BIOF309/datacamp-certificates-ajk5mq repo but I do not see the option to clone this repo into my pycharm. I would like to add a readme file and my pdf files of my certificates into my repo. What should I do?

For some reason we are having trouble converting our markdown file in Juypter to slides.

I did View → Cell Toolbar → Slideshow

Then I selected the ones to be slides and then I typed into my terminal:

jupyter nbconvert Jupyter\ Slides.ipynb --to slides --post serve

However I then received this message:

I cannot seem to convert the slides.

Hi Martin,

Since I was a little behind I have been trying to work as fast as I can to finish before you start grading. Maybe I miss it. I am not sure if we are supposed to create the repo in our own account or one from the class. If is the latter, how exactly do I do that?

Thanks,
Shaimar

Could you help me fix my link to my slides from my readme? I am able to access an interactive presentation from pycharm, but I am unable to do so using my readme link.

code is incorporated into slides but some pdfs of figures are not displaying in slides

If we generate a plot in python how can we include it in our slides.md file?

So I updated to the latest version of pycharm (3.1) last evening and I’m not sure if I did something wrong or not, but each import that I now enter in my file receives an annotation stating that it is an unused import. For instance, when I import pandas as pd, the entire line of code is greyed out with the unused import statement attached. I tried googling I information regarding this, but found it to be a bit unclear. Have you ever encountered something like this?

I tried to add the binder button and link to open my notebook from the markdown file on my repo, but I have not been able to solve the error.

Thank you, Kevin

https://github.com/BIOF309/group-project-rmndr

When running the following code, I run into the following error: RuntimeWarning: divide by zero encountered in true_divide

Code:

outcome = df_merged8.iloc[:, -1]
predictors = df_merged8.iloc[:, 2:-1]

vars_as_str = str(list(predictors.columns)[:25]).replace("'","").replace('[', '').replace(']','').replace(',', ' +')

cox_model = smf.phreg("PERMTH_INT ~ " + vars_as_str, predictors, status=outcome, ties="efron")
results = cox_model.fit()
results.summary()