seandavi GEOquery issues

seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

http://seandavi.github.io/GEOquery/

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issues

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Problems Function Not Found

#105 DarioS closed 3 years ago
2
Parallel Processing on GEOquery

#104 ce-r closed 3 years ago
1
All of the Documentation is Missing

#103 DarioS opened 4 years ago
0
getGEO skipping over header and 616 probes for GSE6691

#102 BJWiley233 closed 3 years ago
3
Fix parsing errors on ^M symbols

#101 assaron closed 3 years ago
0
Error parsing GSE6030_family.soft.gz

#100 ghost closed 3 years ago
1
GSE134381 download error

#99 davidechicco closed 4 years ago
4
AnnotatedDataFrame 'initialize' could not update varMetadata

#98 khughitt opened 4 years ago
0
error in GEOquery

#97 ezgicn closed 4 years ago
4
fix a test that failed with strict boolean check-lengths

#96 russHyde closed 5 years ago
3
Path to urls doesn't work

#95 blancahimes closed 5 years ago
4
getGEO() incorrectly parses GSE6691_series_matrix.txt.gz

#94 khughitt closed 3 years ago
1
GSE27957 parsing failure

#93 bjmt closed 3 years ago
3
findFirstEntity hangs on empty file

#92 assaron closed 2 years ago
1
Downloading gzipped soft files

#91 assaron closed 3 years ago
0
Default amount for soft files

#90 assaron opened 5 years ago
1
Do not freeze on empty files

#89 vlakam closed 5 years ago
1
Recently, I have been having issues with getGEO

#88 swiftiebirth13 closed 5 years ago
3
GSE2193 parsing failure

#87 seandavi closed 3 years ago
3
Error in open.connection(x, "rb") : HTTP error 403.

#86 dfantini82 closed 5 years ago
2
Timeout when use `getGEO`

#85 ShixiangWang closed 5 years ago
4
Converting GSE to an ExpressionSet

#84 JanLanzer opened 5 years ago
0
readr troubles remaining

#83 powestermark closed 3 years ago
1
annotating `!Sample` in function 'parseGSEMatrix'

#82 woolf-wu closed 5 years ago
3
The nature of the downloaded data (normalized vs nonnormalized?)

#81 atakanekiz closed 5 years ago
2
Parsing single cell GSE and get series_table

#80 rjpbonnal opened 5 years ago
2
Switch to data.table (fread) from readr

#79 seandavi closed 3 years ago
1
After current fixes with readr GEOquery fails to parse RNA-seq series

#78 vlakam closed 5 years ago
10
GEOQuery inside of docker

#77 jlevy44 closed 5 years ago
4
getGEO() fails with some GSE records (looks like RNA-seq platforms)

#76 aeolianine closed 5 years ago
4
GEOquery parsing error on GSEs--off-by-one line number.

#75 seandavi closed 5 years ago
5
getGEO recently did not return correct sample names instead return expression values w/ many parsing failures.

#74 zhangj5 closed 5 years ago
1
Added experiment data in GSE

#73 vlakam closed 6 years ago
2
Export `parseGSEMatrix`

#72 hammer closed 6 years ago
2
GEOquery Description Describes Non-Default Functionality

#71 DarioS opened 6 years ago
0
getGEO error when downloading

#70 thyagoleal closed 6 years ago
2
Large number of parsing failures

#69 FarzanT closed 3 years ago
2
getGEOSuppFiles should take a "quiet" argument and pass it to file.download

#68 wobenshain opened 6 years ago
0
Error: Duplicate identifiers for rows (75, 83), (76, 84), (77, 85), (78, 86), (79, 87), (80, 88), (81, 89), (82, 90)

#67 seandavi closed 6 years ago
0
new line in matrix file meta-data breaks functions

#66 kalugny closed 6 years ago
2
getAndParseGSEmatrix minor fix

#65 martinguerrero89 closed 6 years ago
5
Incorrect URL construction

#64 moaraj closed 6 years ago
8
getGEOSuppFiles function bug

#63 ibilgen closed 6 years ago
2
Annotating `!Sample` headers fails

#62 kalugny closed 6 years ago
3
Fixed: Make sure `parseCharacteristics` flag passes

#61 kalugny closed 6 years ago
3
using `parseCharacteristics = FALSE` still parses characteristics

#60 kalugny opened 6 years ago
0
Parsing characteristics failes

#59 kalugny closed 6 years ago
0
GEOquery should recognize non-public accesions

#58 seandavi opened 6 years ago
0
findFirstEntity enters infinite loop on GSEMatrix file stored locally

#57 seandavi closed 6 years ago
0
Added: `parseCharacteristics` flag

#56 kalugny closed 7 years ago
1

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