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markziemann
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dee2
Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
http://dee2.io
GNU General Public License v3.0
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Limit number of parallel cores
#102
markziemann
opened
1 week ago
0
Cannot access homo sapiens dataset on dee2.io
#101
hollywen7
closed
1 year ago
2
prefetch error trying to run the docker container
#100
rcastelo
closed
1 week ago
4
skewer problem
#99
markziemann
closed
1 week ago
0
Docker build fails at RUN pip3 install parallel-fastq-dump
#98
maciejmotyka
closed
2 years ago
4
dee2.io website is down
#97
maciejmotyka
closed
2 years ago
2
Pysradb to fetch SRA metadata?
#96
markziemann
opened
2 years ago
2
Pysam to replace the current metadata fetching system
#95
markziemann
closed
2 years ago
0
cpu speed issue
#94
markziemann
closed
3 years ago
0
redundant line
#93
markziemann
closed
2 years ago
0
DL not stated
#92
markziemann
closed
3 years ago
0
pipeline script md5sum
#91
markziemann
closed
3 years ago
0
issue with started file.
#90
markziemann
closed
3 years ago
0
CODE_DIR specification
#89
markziemann
closed
3 years ago
0
Another problematic wget command to be fixed
#88
markziemann
closed
2 years ago
0
Problem with wget
#87
markziemann
closed
2 years ago
0
Getting the IP
#86
markziemann
closed
2 years ago
0
code/volunteer_pipeline.sh: line 17: [: ==: unary operator expected
#85
markziemann
closed
2 years ago
0
metadata
#84
markziemann
closed
3 years ago
2
GEO series accessions are missing
#83
markziemann
closed
3 years ago
1
degust redirection is broken
#82
markziemann
closed
3 years ago
1
storage on webserver is tight
#81
markziemann
closed
3 years ago
2
Nicer web UI for searching
#80
markziemann
opened
4 years ago
11
More efficient serving SRR in the queue
#79
markziemann
closed
4 years ago
0
QC_summary vs QC_SUMMARY
#78
uilnauyis
closed
4 years ago
7
'getDEE2' function could failed to return DEE2 data if .tsv files contain '#' character
#77
uilnauyis
closed
4 years ago
3
please add COVID-19 data
#76
markziemann
closed
4 years ago
3
GSE accessions are missing
#75
inutano
closed
4 years ago
6
Error in read.table " no lines available in input"
#74
markziemann
closed
4 years ago
1
stricter settings on the shell script volunteer_pipeline.sh
#73
markziemann
closed
4 years ago
0
Permissions issue
#72
markziemann
closed
4 years ago
0
GeneCountMatrix.tsv and TxCountMatrix.tsv are empty downloaded from DEE2
#71
uilnauyis
closed
4 years ago
2
query to http://dee2.io/metadata/hsapiens_metadata.tsv.cut responds 404
#70
uilnauyis
closed
4 years ago
2
SampleName and GSE_accession are identical in hsapiens_metadata.tsv
#69
rcastelo
closed
4 years ago
5
Time to include some extra species
#68
markziemann
opened
4 years ago
6
Datasets larger than 20GB
#67
markziemann
closed
4 years ago
1
Enable users to request missing projects or samples
#66
markziemann
opened
4 years ago
5
Metadata missing some columns
#65
markziemann
closed
4 years ago
0
Make the metadata available on the webserver
#64
markziemann
closed
4 years ago
0
HPC on Gadi
#63
markziemann
closed
4 years ago
1
Make sure all runs in a project have been processed
#62
markziemann
closed
4 years ago
1
Improve queue
#61
markziemann
closed
4 years ago
0
getDEE2 improvements
#60
markziemann
closed
4 years ago
2
NumReadsQcPass bug
#59
markziemann
closed
4 years ago
0
Check that pipeline works with a long list of own fastqs
#58
markziemann
closed
5 years ago
0
memory limitations
#57
markziemann
closed
5 years ago
0
Some datasets are not indexed for download with ASCP
#56
markziemann
closed
5 years ago
1
Integration with Degust
#55
markziemann
closed
5 years ago
1
Replacement to SRAdbV2
#54
markziemann
closed
4 years ago
5
There are some datasets with mapping >100%
#53
markziemann
closed
5 years ago
2
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