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ShortRead
•
reset
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago
danova_fr
▴ 20
14
votes
21
replies
11k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation
shortread
dependency
updated 4.9 years ago by
January Weiner
▴ 240 • written 6.0 years ago by
joseph.elsherbini
▴ 60
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.6 years ago
patrick.schordert
▴ 30
0
votes
5
replies
1.9k
views
read coverage per transcript for RNASeq
RNASeq
Coverage
PROcess
ShortRead
RNASeq
Coverage
PROcess
ShortRead
updated 14.6 years ago by
Martin Morgan
25k • written 14.7 years ago by
Jessica Hunter
▴ 40
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
kelvinfrog75
• 0
12
votes
7
replies
1.9k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql
shortread
Rsubread
updated 5.0 years ago by
Aspie96
▴ 60 • written 5.1 years ago by
Raito92
▴ 60
0
votes
11
replies
2.3k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges
ShortRead
nucleR
IRanges
ShortRead
nucleR
12.5 years ago
Stefanie Ververs
▴ 70
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread
fastq
9.0 years ago
danova_fr
▴ 20
0
votes
2
replies
1.7k
views
Solexa fastq files and BLAT
Cancer
Biostrings
ShortRead
Cancer
Biostrings
ShortRead
updated 5.3 years ago by
Bioconductor Community
0 • written 15.3 years ago by
Daniel Brewer
★ 1.9k
0
votes
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis
rsamtools
shortread
biostrings
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
travis.m.couture
• 0
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.6 years ago
David
▴ 860
0
votes
3
replies
1.7k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread
readAligned
reverseComplement
ScanBamParam
9.3 years ago
jdavison
▴ 10
4
votes
5
replies
1.7k
views
No BAM option in readAligned from the ShortRead package
bioconductor
shortread
bam file
nucler
updated 6.2 years ago by
Dario Strbenac
★ 1.5k • written 6.2 years ago by
jfgout
▴ 10
0
votes
2
replies
1.2k
views
mismatch & replacement
ShortRead
ShortRead
updated 13.5 years ago by
Harris A. Jaffee
▴ 590 • written 13.5 years ago by
Daniel.Berner@unibas.ch
▴ 90
0
votes
4
replies
1.4k
views
ShortRead for sequencing data quality assessment
Sequencing
ShortRead
Sequencing
ShortRead
13.6 years ago
heyi xiao
▴ 360
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread
illumina
9.1 years ago
danova_fr
▴ 20
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread
biostrings
5.6 years ago
ferbecneu
• 0
0
votes
2
replies
1.4k
views
readFastq error reading Nanopore fastq
shortread
6.7 years ago • updated 6.6 years ago
kamal.fartiyal84
▴ 10
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago
danova_fr
▴ 20
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead
ShortRead
updated 11.4 years ago by
Martin Morgan
25k • written 11.4 years ago by
Ivan Gregoretti
▴ 310
0
votes
3
replies
1.3k
views
ShortRead QA
Sequencing
ShortRead
Sequencing
ShortRead
updated 13.8 years ago by
Martin Morgan
25k • written 13.8 years ago by
Alex Gutteridge
▴ 650
0
votes
2
replies
1.1k
views
pileup function in ShortRead package
Alignment
ShortRead
Alignment
ShortRead
updated 14.6 years ago by
Martin Morgan
25k • written 14.5 years ago by
Nora Rieber
▴ 40
0
votes
1
reply
640
views
report a possible bug of
ShortRead
ShortRead
updated 12.2 years ago by
Martin Morgan
25k • written 12.2 years ago by
wang peter
★ 2.0k
0
votes
1
reply
766
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead
ShortRead
updated 11.9 years ago by
Martin Morgan
25k • written 11.9 years ago by
talshay
▴ 10
0
votes
1
reply
827
views
ShortRead package
ShortRead
ShortRead
updated 11.8 years ago by
Martin Morgan
25k • written 11.8 years ago by
Fatemehsadat Seyednasrollah
▴ 260
0
votes
1
reply
827
views
how to plot quality report
ShortRead
ShortRead
updated 11.7 years ago by
Martin Morgan
25k • written 11.7 years ago by
wang peter
★ 2.0k
0
votes
1
reply
1.1k
views
trimTails function in ShortRead package give different results on the same input
Sequencing
ShortRead
Sequencing
ShortRead
updated 11.5 years ago by
Martin Morgan
25k • written 11.5 years ago by
Zhenyu Xu
▴ 10
0
votes
4
replies
949
views
how to get the quality score system information from the reads
ShortRead
ShortRead
updated 11.5 years ago by
Martin Morgan
25k • written 11.5 years ago by
wang peter
★ 2.0k
0
votes
3
replies
6.0k
views
readFasta and gzipped FASTA files
ShortRead
ShortRead
updated 11.2 years ago by
Martin Morgan
25k • written 11.2 years ago by
Ivan Gregoretti
▴ 310
0
votes
3
replies
2.6k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing
ShortRead
Preprocessing
ShortRead
updated 11.2 years ago by
Martin Morgan
25k • written 11.2 years ago by
Noah Dowell
▴ 410
0
votes
3
replies
2.2k
views
bioc package installation problem
ShortRead
BiocInstaller
ShortRead
BiocInstaller
updated 11.0 years ago by
Dan Tenenbaum
★ 8.2k • written 11.0 years ago by
carol white
▴ 680
0
votes
5
replies
1.5k
views
Finding my un-counted reads
Sequencing
rtracklayer
ShortRead
GenomicRanges
Sequencing
rtracklayer
ShortRead
updated 10.7 years ago by
Valerie Obenchain
★ 6.8k • written 10.7 years ago by
Sam McInturf
▴ 300
0
votes
2
replies
3.1k
views
ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess
ShortRead
PROcess
ShortRead
updated 10.4 years ago by
Martin Morgan
25k • written 10.4 years ago by
Sam McInturf
▴ 300
0
votes
3
replies
2.7k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 9.3 years ago by
Valerie Obenchain
★ 6.8k • written 9.3 years ago by
newmanss
• 0
5
votes
1
reply
3.1k
views
fastqSampler and writeFastq in shortread package
shortread
fastq
write
updated 9.2 years ago by
Martin Morgan
25k • written 9.2 years ago by
francesca.defilippis
▴ 100
5
votes
4
replies
3.2k
views
Trimming with ShortRead
shortread
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
cookie
▴ 20
1
vote
2
replies
2.2k
views
FastqSampler with trimmed paired-end reads
shortread
updated 3.2 years ago by
robmaz77
▴ 20 • written 8.8 years ago by
Arne Muller
▴ 20
1
vote
2
replies
1.6k
views
Why I'm getting an error when using ShortRead package's FastqStreamerList function?
shortread
fastqSteamerList
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
simonas.juzenas
▴ 10
1
vote
1
reply
1.0k
views
error: incorrect number of fields (1) input.bam:1
shortread
readaligned
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
kspata
▴ 10
0
votes
1
reply
1.0k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead
ShortRead
updated 13.3 years ago by
Martin Morgan
25k • written 13.3 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
1.2k
views
FastqSampler sort by ID
ShortRead
ShortRead
updated 11.4 years ago by
Martin Morgan
25k • written 11.4 years ago by
Marcus Davy
▴ 390
0
votes
1
reply
726
views
Vignette for ShortRead
ShortRead
ShortRead
updated 15.8 years ago by
Martin Morgan
25k • written 15.8 years ago by
joseph
▴ 330
0
votes
1
reply
875
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer
PROcess
ShortRead
charm
Cancer
PROcess
ShortRead
charm
15.1 years ago
Martin Morgan
25k
0
votes
1
reply
792
views
possible bug in extendReads() in package chipseq
Alignment
ShortRead
Alignment
ShortRead
updated 14.4 years ago by
Martin Morgan
25k • written 14.4 years ago by
Nora Rieber
▴ 40
0
votes
2
replies
908
views
ShortRead internal: too many 'snap' entries
ShortRead
ShortRead
updated 14.3 years ago by
Martin Morgan
25k • written 14.3 years ago by
Ramzi TEMANNI
▴ 160
0
votes
1
reply
902
views
Shortread and filtering of duplicate reads
ShortRead
ShortRead
updated 14.3 years ago by
Martin Morgan
25k • written 14.3 years ago by
Johannes Waage
▴ 50
0
votes
2
replies
981
views
ShortRead with BAM
ShortRead
ShortRead
updated 14.0 years ago by
James W. MacDonald
65k • written 14.0 years ago by
Duke
▴ 210
0
votes
1
reply
728
views
Typo in ?FastqQuality help page?
ShortRead
ShortRead
updated 13.9 years ago by
Martin Morgan
25k • written 13.9 years ago by
Peng Yu
▴ 940
0
votes
1
reply
1.0k
views
ShortRead information
ShortRead
ShortRead
updated 13.9 years ago by
Martin Morgan
25k • written 13.9 years ago by
Jennifer Dupiot
▴ 10
0
votes
3
replies
2.0k
views
Error installing Rsamtools
ShortRead
Rsamtools
ShortRead
Rsamtools
updated 13.9 years ago by
Martin Morgan
25k • written 13.9 years ago by
Paul Geeleher
★ 1.3k
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Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
Yes, I'm working only with genes from terpenoids pathway (14 genes), so I can't use enrichGO? Can you recommend a package or something like…
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
Your awnser at Cannabis orgDb solve my problems using enrichGO by far. I'm underdegree biotechnology student, and I learning bioinformatic…
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★ 3.9k
It is indeed better. Anyway, did you notice this part in the output from `str(ortologos_filtrados)`: `$Gene.ID : int 115709372 115716460 …
Comment: Trying to use enrichGO
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I'm new here, but its better now?
Comment: Trying to use enrichGO
by
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★ 3.9k
That did NOT really improve things...... Likely I wasn't clear enough, but with R-code I meant both the command you typed, as well as the o…
Votes
Comment: Trying to use enrichGO
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DESeq2: How to find out how well the model fits the data?
Comment: DESeq2 - dispersion estimation when there is none
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