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sradb
•
reset
0
votes
0
replies
159
views
Best straightforward way from SRA-fastq to Phyloseq Object
SRAdb
8 months ago
Davide
• 0
7
votes
3
replies
4.0k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
7.0 years ago • updated 10 months ago
Sean Davis
21k
0
votes
3
replies
363
views
getSRA() from the SRAdb package is returning an empty data.frame from the full SQL file, but not the demo file
SRAdb
getSRA()
updated 20 months ago by
James W. MacDonald
59k • written 20 months ago by
mac54
• 0
0
votes
0
replies
441
views
listSRAfile: Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
SRAdb
2.0 years ago
Aditya
▴ 140
0
votes
0
replies
485
views
Query based on PMIDs
SRAdb
geoquery
3.5 years ago
Deepak Tanwar
▴ 10
2
votes
0
replies
588
views
Discrepancies between sradb, sraruninfo
sradb
4.0 years ago
langmea
▴ 20
1
vote
2
replies
1.8k
views
SRAdb: Error downloading sqlite files
sradb
4.5 years ago
arielle
• 0
1
vote
3
replies
1.1k
views
problem with getSRAfile in SRAdb
SRAdb
updated 4.5 years ago by
Jack Zhu
▴ 170 • written 4.5 years ago by
shidaxia
• 0
0
votes
8
replies
2.4k
views
error in SRAdb
SRAdb
SRAdb
updated 4.6 years ago by
djlemas
• 0 • written 7.8 years ago by
Faryabi, Robert NIH/NCI [F]
▴ 30
2
votes
1
reply
736
views
Uniting SRA Data into a single file
R
fastq
SRA
sradb
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
grecoandreauni
• 0
0
votes
1
reply
1.1k
views
Empty SQL query result for SRA run
sradb
5.6 years ago
Thomas Sandmann
▴ 80
0
votes
2
replies
836
views
SRAdb "outdated" sqlite db
sradb
sqlite
outdated
updated 5.6 years ago by
Sean Davis
21k • written 5.7 years ago by
Nicolas Delhomme
▴ 320
0
votes
1
reply
1.3k
views
Error downloading using SRAdb
fastq
sradb
ftp
updated 6.2 years ago by
Jack Zhu
▴ 170 • written 6.2 years ago by
yugi1001
• 0
2
votes
2
replies
1.3k
views
SRAdb: could not find function "sqliteTableFields"
sradb
sqlite
updated 7.5 years ago by
Sean Davis
21k • written 7.5 years ago by
dario.beraldi
• 0
0
votes
1
reply
848
views
Analysis of Next Generation of Sequencing DAta
SRAdb
updated 7.6 years ago by
Sean Davis
21k • written 7.6 years ago by
Jerry Cholo
▴ 190
0
votes
0
replies
896
views
SRAmetadb Bioconductor package; study record count low for 2013
SRAdb
SRAdb
7.9 years ago
Hugh Shanahan
▴ 50
0
votes
2
replies
1.1k
views
SRAmetadb Bioconductor package; study record count low for 2013
SRAdb
SRAdb
updated 7.9 years ago by
Jack Zhu
▴ 170 • written 8.0 years ago by
Al-Nasir, Jamie 2012
▴ 10
0
votes
0
replies
1.7k
views
SRAdb package - problems
Genetics
SRAdb
Genetics
SRAdb
8.9 years ago
Jack Zhu
▴ 170
0
votes
0
replies
1.0k
views
Is it possible to get SRA sample attributes for a given sample or experiment ID?
SRAdb
SRAdb
9.1 years ago
Vladimir Morozov
▴ 130
0
votes
2
replies
1.4k
views
getSRAdbFile cannot open URL
SRAdb
SRAdb
updated 9.7 years ago by
Martin Morgan
25k • written 9.7 years ago by
Nicholas Stong
▴ 10
0
votes
0
replies
817
views
SRAdb: differences between the database and the NCBI website
PROcess
SRAdb
PROcess
SRAdb
9.9 years ago
Ben Woodcroft
▴ 40
0
votes
1
reply
860
views
SRAdb: is the database missing some entries? (Ben Woodcroft)
SRAdb
SRAdb
updated 9.9 years ago by
Ben Woodcroft
▴ 40 • written 9.9 years ago by
Jack Zhu
▴ 170
0
votes
0
replies
956
views
Cevap: Re: SRAdb error
SRAdb
SRAdb
10.1 years ago
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
1.2k
views
SRAdb error
SRAdb
SRAdb
updated 10.2 years ago by
Sean Davis
21k • written 10.2 years ago by
Ayten YIGITER
▴ 10
0
votes
0
replies
1.1k
views
Bioconductor Digest, Vol 95, Issue 7
PROcess
SRAdb
PROcess
SRAdb
11.4 years ago
Jack Zhu
▴ 170
0
votes
2
replies
916
views
SRAdb listFastq error
SRAdb
SRAdb
updated 11.4 years ago by
Sean Davis
21k • written 11.4 years ago by
Mark Dunning
★ 1.1k
0
votes
8
replies
1.3k
views
'SRAdb useful for visualizing BAM files'
SRAdb
SRAdb
updated 12.1 years ago by
Jack Zhu
▴ 170 • written 12.1 years ago by
Paul Shannon
★ 1.1k
27 results • Page
1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
Yang Shi
• 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available
by
swbarnes2
★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
James W. MacDonald
59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
by
Rory Stark
★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
by
Yang Shi
• 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Use MulticoreParam under BatchtoolsParam
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
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Johannes Rainer
★ 1.9k
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to
Gordon Smyth
45k
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to
Julie Zhu
★ 4.3k
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Hervé Pagès
15k
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James W. MacDonald
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