zebrafish example bug #2
Comments
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Hi Altynai! The zebrafish notebook is the only one where there is no public data at this stage - all other notebooks can be executed. The data has been sent out by email from the lab. @calebweinreb, are you or dan (he is probably not on github, right?) planning to upload the files that you shared at the time somewhere? Would you mind if I upload them somewhere so that the notebook becomes executable? |
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Hi Alex,
As far as I know, you are free to upload the files and host them however
you want want since the paper is published. Let me know if you need us to
send the files again. I am pretty sure we have also uploaded them
somewhere- maybe Dan can comment on that.
…-- Caleb
On Thu, Jan 24, 2019 at 3:14 PM Alex Wolf ***@***.***> wrote:
Hi Altynai! The zebrafish notebook is the only one where there is no
public data at this stage - all other notebooks can be executed. The data
has been sent out by email from the lab. @calebweinreb
<https://github.com/calebweinreb>, are you or dan (he is probably not on
github, right?) planning to upload the files that you shared at the time
somewhere? Would you mind if I upload them somewhere so that the notebook
becomes executable?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
<#2 (comment)>, or mute
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.
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Hi Caleb & Alex,
Yes, Caleb is correct. The files are publicly available in multiple
formats from the locations linked below. I am not sure if a more specific
format/version would be needed for seamless integration with Alex's PAGA
notebook. Please let me know if I could help with that. I am also happy
to upload any additional such files to our Kleintools web portal, which
could then be easily linked to from your Github.
Best,
Dan
GEO:
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112294
Kleintools web portal:
http://www.tinyurl.com/scZfish2018
Other Matlab and h5ad versions of the dataset:
https://kleintools.hms.harvard.edu/paper_websites/wagner_zebrafish_timecourse2018/WagnerScience2018.mat
https://kleintools.hms.harvard.edu/paper_websites/wagner_zebrafish_timecourse2018/WagnerScience2018.h5ad
…On Thu, Jan 24, 2019 at 3:23 PM Caleb Weinreb ***@***.***> wrote:
Hi Alex,
As far as I know, you are free to upload the files and host them however
you want want since the paper is published. Let me know if you need us to
send the files again. I am pretty sure we have also uploaded them
somewhere- maybe Dan can comment on that.
-- Caleb
On Thu, Jan 24, 2019 at 3:14 PM Alex Wolf ***@***.***>
wrote:
> Hi Altynai! The zebrafish notebook is the only one where there is no
> public data at this stage - all other notebooks can be executed. The data
> has been sent out by email from the lab. @calebweinreb
> <https://github.com/calebweinreb>, are you or dan (he is probably not on
> github, right?) planning to upload the files that you shared at the time
> somewhere? Would you mind if I upload them somewhere so that the notebook
> becomes executable?
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#2 (comment)>, or mute
> the thread
> <https://github.com/notifications/unsubscribe-auth/AF3OsnmFntcnbB9Qsy46CW1osqB4-wo3ks5vGhQ0gaJpZM4aQ2UU>
> .
>
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Ah, nice! h5ad even. This should make it trivial to include a line like adata = sc.read('WagnerScience2018', backup_url='https://kleintools.hms.harvard.edu/paper_websites/wagner_zebrafish_timecourse2018/WagnerScience2018.h5ad')right? No |
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Awesome, @calebweinreb & Dan, thanks for the quick answer! And so cool that you uploaded an As the uploaded h5ad doesn't contain the single-cell graph, however, the material is not enough to run the PAGA notebook here. What Caleb sent me around May consisted in these files: What misses is essentially the graph that underlies the figures in your paper and the SPRING-based exploration, which saved me (saves the people trying to reproduce the notebook) from doing all the preprocessing and graph computation. It be really cool if the graph was publicly available. For this, one could either upload a compressed version of the files (as shared via email at the time). Or one could upload an AnnData object that contains the graph. The only problem I see is that the current https://kleintools.hms.harvard.edu/paper_websites/wagner_zebrafish_timecourse2018/WagnerScience2018.h5ad seems to contain unfiltered data with 63530 cells, whereas the graph that Caleb sent out contains 53181 cells. I don't know whether you'd want me to send you this AnnData, which contains the graph. You could upload it as |
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If you don't want me to send you the AnnData containing the graph, I'm also happy to upload the data somewhere else. But the canonical location would be your web page, I guess. 🙂 |
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Hello, I've been following the thread and was also interested in reproducing the PAGA notebook with the zebrafish dataset but still couldn't find any of the additional files needed to run the notebook. Any information on how to obtain them would be greatly appreciated. Thanks in advance. |
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How can I get the additional files that I can run the zebrafish notebook successfully?Could anyone help with this? Thanks in advance! |
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Sorry for the late response on this. I uploaded the files that @calebweinreb sent out via email here: https://drive.google.com/file/d/1V2xA9P1nTaO9qWPj8LiAR-uQpqg0VMBv/view?usp=sharing I'll also make a note on the notebook. |
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Here is the note on the notebook: b5dfcff |
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Hi, I try to replicate zebrafish.ipynb, but encounter some errors.
Also, I try to directly use the Anndata object Could you please help me to figure this out? Thanks |
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Im having the same issue as @kangbw702 |
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Joining in late: 2 - The difference in cell numbers is probably due to some filtering. In the original dataset there is the wildtype experiment (36749 cells) TraceSeq experiment (another ~30k cells), all from 24hpf. 3 - Regarding the missing |
sorry, I'm coming too late so the link you have shared is unavailable. Can you share it again? Thanks! |
I tried to run the zebrafish notebook and received this error message
>>>var = pd.read_csv('./data/gene_names.txt', index_col=0, header=None) --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) <ipython-input-8-3cb7686bdda8> in <module> ----> 1 var = pd.read_csv('./data/gene_names.txt', index_col=0, header=None) C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skipfooter, doublequote, delim_whitespace, low_memory, memory_map, float_precision) 676 skip_blank_lines=skip_blank_lines) 677 --> 678 return _read(filepath_or_buffer, kwds) 679 680 parser_f.__name__ = name C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 438 439 # Create the parser. --> 440 parser = TextFileReader(filepath_or_buffer, **kwds) 441 442 if chunksize or iterator: C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in __init__(self, f, engine, **kwds) 785 self.options['has_index_names'] = kwds['has_index_names'] 786 --> 787 self._make_engine(self.engine) 788 789 def close(self): C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in _make_engine(self, engine) 1012 def _make_engine(self, engine='c'): 1013 if engine == 'c': -> 1014 self._engine = CParserWrapper(self.f, **self.options) 1015 else: 1016 if engine == 'python': C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\parsers.py in __init__(self, src, **kwds) 1706 kwds['usecols'] = self.usecols 1707 -> 1708 self._reader = parsers.TextReader(src, **kwds) 1709 1710 passed_names = self.names is None pandas\_libs\parsers.pyx in pandas._libs.parsers.TextReader.__cinit__() pandas\_libs\parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() FileNotFoundError: File b'./data/gene_names.txt' does not existThe text was updated successfully, but these errors were encountered: