Code availability? - Githubissues

kobeho24 commented 5 years ago

Just wonder if the code for analysis would be available any time soon. I downloaded the processed data of droplet scRNA-seq in h5ad. Need some info about how the raw data was processed to do some downstream analysis.

Cheers, Gary

NMinato77 commented 4 years ago

I am also working on the processed data, and need more information to analyze them properly. For example, why are there no mitochondrial genes in the count matrix? Why are the numbers of cell types in the data different from those on the interactive web page? Could you give us more details about how the data were processed?

Best, Minato

aopisco commented 4 years ago

@NMinato77 thank you for the reminder. The reference genome we used did not contain mitochondrial genes but I'm working on making those available. The interactive browser is currently being updated with the objects you can find here: https://s3.console.aws.amazon.com/s3/buckets/czb-tabula-muris-senis/Data-objects/?region=us-west-2 As for the processing the revised manuscript (https://www.biorxiv.org/content/10.1101/661728v2) contains a diagram in EDFig2 with the steps and the code will be made available shortly.

NMinato77 commented 4 years ago

@aopisco Thank you very much for your quick reply; this is very helpful. I continue to work on and make the most of your precious data, and look forward to the update.

Best, Minato

NMinato77 commented 4 years ago

@aopisco I have tried the following two objects on AWS: tabula-muris-senis-droplet-raw-official-annotations.h5ad tabula_sc/tabula-muris-senis-droplet-raw-official-annotations.h5ad

However, I've got AttributeError like below on both of them. Are they broken?

raw_data = sc.read_h5ad("tabula-muris-senis-droplet-raw-official-annotations.h5ad")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/dice1988/anaconda3/envs/mt/lib/python3.7/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
    constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
  File "/home/dice1988/anaconda3/envs/mt/lib/python3.7/site-packages/anndata/readwrite/read.py", line 502, in _read_args_from_h5ad
    return AnnData._args_from_dict(d)
  File "/home/dice1988/anaconda3/envs/mt/lib/python3.7/site-packages/anndata/core/anndata.py", line 2157, in _args_from_dict
    if key in d_true_keys[true_key].dtype.names:

AttributeError: 'dict' object has no attribute 'dtype'

Best, Minato

aopisco commented 4 years ago

@NMinato77 I've just updated the objects in there. Can you please try again? Sorry for this!

NMinato77 commented 4 years ago

@aopisco Are they public? I cannot download them. It says

This XML file does not appear to have any style information associated with it. The document tree is shown below.
<Error>
<Code>AccessDenied</Code>
<Message>Access Denied</Message>
<RequestId>D7B31D75CD0671FB</RequestId>
<HostId>
/xCMV15Rp1L/seABHNi9mEOvQdt9wJ82uum0KnO61Nc/IWqQN/sVwyjHckRLr4Dpbm8pAu8TVgA=
</HostId>
</Error>

and the access is denied.

aopisco commented 4 years ago

I made the whole folder public again - please let me know if you still have problems.

NMinato77 commented 4 years ago

@aopisco Finally, they work; I successfully downloaded them and loaded them. Thank you very much for your kind and quick help.

aopisco commented 4 years ago

@kobeho24 let me know if the jupyter notebooks now available are easy to read and work with

czbiohub-sf / tabula-muris-senis

Code availability? #1