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Showing :
shortread
•
reset
4
votes
7
replies
1.9k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
15 months ago • updated 14 months ago
Bernardo
▴ 10
0
votes
3
replies
1.2k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4
ShortRead
18 months ago
Bogdan
▴ 670
1
vote
1
reply
848
views
Unable to install "scruff" with BiocManager::install()
scruff
Install
ShortRead
updated 19 months ago by
shepherl
3.8k • written 19 months ago by
Jackson
• 0
1
vote
3
replies
830
views
support for reading direct RNA-Seq FASTQs
ShortRead
nanopore
24 months ago
kent.riemondy
▴ 20
0
votes
4
replies
1.1k
views
BiocParallel: bplapply invents data
BiocParallel
ShortRead
3.1 years ago
robmaz77
▴ 20
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
3.2 years ago
robmaz77
▴ 20
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by
Daniel.Berner@unibas.ch
▴ 90
0
votes
3
replies
1.3k
views
ShortRead: how to convert qualities?
ShortRead
FastqQuality
3.2 years ago
robmaz77
▴ 20
0
votes
2
replies
1.6k
views
Cannot Install ShortRead Package
ShortRead
written 3.4 years ago by
Bob
• 0
0
votes
7
replies
2.2k
views
Cannot install ShortRead package
ShortRead
updated 3.4 years ago by
Martin Morgan
25k • written 3.4 years ago by
Bob
• 0
0
votes
3
replies
1.3k
views
ShortRead Error message: invalid character '
shortread
fastq
4.5 years ago
lauren.fitch
• 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 5.0 years ago by
Raito92
▴ 60
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
1
vote
3
replies
1.4k
views
Remove reads from raw fastq
shortread
biostrings
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
ferbecneu
• 0
0
votes
4
replies
3.6k
views
Retrieving specific sequences from a fastq
shortread
biostrings
5.5 years ago
ferbecneu
• 0
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 5.9 years ago by
joseph.elsherbini
▴ 60
0
votes
4
replies
939
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
Frocha
▴ 20
4
votes
3
replies
1.5k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread
pacbio
fastq
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
benjamin.j.callahan
▴ 50
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
1
vote
2
replies
1.2k
views
bplapply with ShortRead functions
shortread
biocparallel
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
Vivek.b
▴ 100
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead
FastqStreamer
6.4 years ago
ioannis.vardaxis
▴ 30
0
votes
2
replies
1.4k
views
readFastq error reading Nanopore fastq
shortread
6.6 years ago
kamal.fartiyal84
▴ 10
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings
shortread
updated 7.0 years ago by
Hervé Pagès
16k • written 7.0 years ago by
jma1991
▴ 70
3
votes
10
replies
4.4k
views
How to check that the reads in two fastq files are in the same order
shortread
fastq
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
Frocha
▴ 20
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.6 years ago
David
▴ 860
1
vote
2
replies
1.4k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 7.7 years ago by
Martin Morgan
25k • written 7.7 years ago by
Radek
▴ 90
0
votes
1
reply
1.2k
views
make: *** [ShortRead.so] Error 1
shortread
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
mictadlo
▴ 10
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
5
votes
1
reply
3.2k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
8.0 years ago
phil.chapman
▴ 150
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
phil.chapman
▴ 150
5
votes
7
replies
2.3k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
chapmandu2
▴ 20
0
votes
0
replies
1.2k
views
Error with qa() in package ShortRead when checking for adapter contamination.
shortread
8.2 years ago
Diego Diez
▴ 760
0
votes
1
reply
1.2k
views
ShortRead::FastqStreamer() causes segfault
shortread
segfault
8.3 years ago
Watal M. Iwasaki
▴ 10
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges
shortread
Biostrings
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
pavitrarc
▴ 20
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing
biostrings
shortread
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
steven.everman
▴ 10
0
votes
2
replies
1.5k
views
ShortRead Error in slot(object, ".srlist")
software error
ShortRead
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
sbrown36
• 0
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
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
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago
danova_fr
▴ 20
0
votes
4
replies
1.6k
views
gcContent error with shortread
shortread
9.0 years ago
danova_fr
▴ 20
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread
fastq
9.0 years ago
danova_fr
▴ 20
5
votes
4
replies
3.2k
views
Trimming with ShortRead
shortread
updated 9.0 years ago by
Martin Morgan
25k • written 9.1 years ago by
cookie
▴ 20
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread
illumina
9.1 years ago
danova_fr
▴ 20
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
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
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
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
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
0
replies
972
views
Longest continuous sequence from multiple alignment
GO
ShortRead
GO
ShortRead
10.0 years ago
Guest User
★ 13k
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
50 results • Page
1 of 1
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Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
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