guma44 GEOparse issues - Githubissues

guma44 / GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

BSD 3-Clause "New" or "Revised" License

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issues

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Fix failing tests: Add compatibility with pandas 2

#85 olp-cs opened 4 months ago
0
Failing test: `test_merge_and_average` fails with a TypeError with pandas 2.0.3

#84 olp-cs opened 4 months ago
0
Fix issue when GEO metadata contains commas

#83 alexbarrera closed 7 months ago
1
UnboundLocalError when GSE non-existent

#82 jonasfreimuth opened 1 year ago
1
download all supplementary file instead of only one

#81 BioInfoData closed 7 months ago
0
download fails because of content-length mismatch when content-encoding=gzip

#80 vttrifonov opened 2 years ago
1
Summary GSM metadata table

#79 RemyLau opened 2 years ago
0
Skip conversion to fastq if existing

#78 hschult opened 3 years ago
0
Declare total_size outside of try block so it can't be undeclared.

#77 kurtwheeler closed 7 months ago
0
Suggestion for an improvement of the GEOparse.utils.smart_open() function

#76 abysslover opened 3 years ago
0
Suggestion for an improvement of the GEOparse.__parse_entry() function

#75 abysslover opened 3 years ago
0
Phenotype data does not use pandas dtype inference

#74 hardingnj opened 3 years ago
1
Fixes typo in documentation

#73 MichaelLampe closed 3 years ago
1
GEOparse not downloading a supplementary file for a GSE

#72 grisaitis opened 3 years ago
0
fix typo with print function in usage

#71 grisaitis closed 3 years ago
5
DtypeWarning: Columns (7) have mixed types.

#70 CholoTook opened 3 years ago
4
Am I doin it rong?

#69 CholoTook opened 3 years ago
1
using merge_and_average with annotation

#68 tyasird closed 3 years ago
1
is there any way to re-write downloaded files?

#67 tyasird closed 3 years ago
1
is there any way to get GSM sample names without full download?

#66 tyasird closed 3 years ago
5
UnboundLocalError while trying the example from documentation

#65 sowmyamanojna opened 3 years ago
2
BUGFIX: shutil.move can lead to "operation not permitted" error

#64 mvonpapen closed 3 years ago
1
Allow the file encoding to be specified in smart_open()

#63 ghost closed 4 years ago
3
cannot download and parse GEO files

#62 Mengflz opened 4 years ago
11
Can you read XML files with this tool?

#61 jolespin closed 4 years ago
1
Check if GSE entry is public

#60 adirot closed 4 years ago
2
Debugging everything

#59 liugaocn closed 5 years ago
3
Warning if fastq-dump is not installed or on $PATH

#58 JohnWSteill opened 5 years ago
1
gsm2fastq: allow for dynamic allocation of threads

#57 Maarten-vd-Sande closed 5 years ago
0
Develop

#56 guma44 closed 5 years ago
1
Parallel fastq

#55 simonvh closed 5 years ago
1
Add partial arg to parse_GPL and get_GEO. #53

#54 ttyskg closed 5 years ago
3
Partially parsing of large GPL file

#53 ttyskg closed 5 years ago
2
Replace ix to loc

#52 ttyskg closed 5 years ago
1
Missing File Error when GEO is Down

#51 Miserlou opened 5 years ago
1
ValueError when trying to reproduce tutorials

#50 CiaranWelsh closed 6 years ago
1
Add Timeout to urlopen Calls

#49 Miserlou closed 6 years ago
1
Cut a New Release?

#48 Miserlou closed 6 years ago
3
GEOparse.logger.set_verbosity doesn't work

#47 Miserlou closed 6 years ago
2
wgetter/urlget have no timeouts

#46 Miserlou closed 6 years ago
1
use `pandas.read_csv` rather than `DataFrame.from_csv`

#45 Miserlou closed 6 years ago
2
Library citation for scientific paper

#44 agalitsyna closed 6 years ago
1
Parallel download

#43 agalitsyna closed 6 years ago
5
showing all SRRs for a particular GSM

#42 golobor opened 6 years ago
1
Remove downloaded archive // Cleanup

#41 Miserlou opened 6 years ago
1
Download MINiML

#40 Miserlou opened 6 years ago
1
parallel fastq_dump support

#39 antonkulaga closed 6 years ago
1
Broken download when supplementary_files is empty or contains invalid URLs

#38 antonkulaga closed 6 years ago
7
SRR type now known

#37 antonkulaga opened 6 years ago
1
Some samples don't have table data!

#36 halioui opened 6 years ago
6