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Showing :
shortread
•
reset
4
votes
7
replies
1.8k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq
LongRead
Normalization
ShortRead
IlluminaRNASeq
14 months ago • updated 13 months ago
Bernardo
▴ 10
0
votes
3
replies
1.2k
views
ShortRead Installation in R 4.2.0 and zlib library
R-4
ShortRead
17 months ago
Bogdan
▴ 670
1
vote
1
reply
809
views
Unable to install "scruff" with BiocManager::install()
scruff
Install
ShortRead
updated 18 months ago by
shepherl
3.8k • written 18 months ago by
Jackson
• 0
1
vote
3
replies
798
views
support for reading direct RNA-Seq FASTQs
ShortRead
nanopore
23 months ago
kent.riemondy
▴ 20
0
votes
4
replies
1.0k
views
BiocParallel: bplapply invents data
BiocParallel
ShortRead
3.0 years ago
robmaz77
▴ 20
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
3.1 years ago
robmaz77
▴ 20
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.1 years ago by
Daniel.Berner@unibas.ch
▴ 90
0
votes
3
replies
1.2k
views
ShortRead: how to convert qualities?
ShortRead
FastqQuality
3.1 years ago
robmaz77
▴ 20
0
votes
2
replies
1.5k
views
Cannot Install ShortRead Package
ShortRead
written 3.3 years ago by
Bob
• 0
0
votes
7
replies
2.2k
views
Cannot install ShortRead package
ShortRead
updated 3.3 years ago by
Martin Morgan
25k • written 3.3 years ago by
Bob
• 0
0
votes
3
replies
1.2k
views
ShortRead Error message: invalid character '
shortread
fastq
4.4 years ago
lauren.fitch
• 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 4.8 years ago by
January Weiner
▴ 240 • written 5.9 years ago by
joseph.elsherbini
▴ 60
12
votes
7
replies
1.8k
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
0
votes
2
replies
1.7k
views
Solexa fastq files and BLAT
Cancer
Biostrings
ShortRead
Cancer
Biostrings
ShortRead
updated 5.2 years ago by
Bioconductor Community
0 • written 15.2 years ago by
Daniel Brewer
★ 1.9k
1
vote
1
reply
989
views
error: incorrect number of fields (1) input.bam:1
shortread
readaligned
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 years ago by
kspata
▴ 10
1
vote
3
replies
1.3k
views
Remove reads from raw fastq
shortread
biostrings
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
ferbecneu
• 0
0
votes
4
replies
3.5k
views
Retrieving specific sequences from a fastq
shortread
biostrings
5.5 years ago
ferbecneu
• 0
0
votes
4
replies
911
views
Should I use legacy functions in ShortRead package?
shortread
updated 6.0 years ago by
Martin Morgan
25k • written 6.0 years ago by
Frocha
▴ 20
4
votes
3
replies
1.4k
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread
pacbio
fastq
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 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 6.1 years ago by
Dario Strbenac
★ 1.5k • written 6.1 years ago by
jfgout
▴ 10
1
vote
2
replies
1.2k
views
bplapply with ShortRead functions
shortread
biocparallel
updated 6.1 years ago by
Martin Morgan
25k • written 6.1 years ago by
Vivek.b
▴ 100
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead
FastqStreamer
6.3 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
2.6k
views
strsplit method for DNAStringSet objects
biostrings
shortread
updated 6.9 years ago by
Hervé Pagès
16k • written 6.9 years ago by
jma1991
▴ 70
3
votes
10
replies
4.3k
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
7.5 years ago
David
▴ 860
1
vote
2
replies
1.4k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 7.6 years ago by
Martin Morgan
25k • written 7.6 years ago by
Radek
▴ 90
0
votes
1
reply
1.1k
views
make: *** [ShortRead.so] Error 1
shortread
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
mictadlo
▴ 10
0
votes
5
replies
1.3k
views
Error Raised When Trying To Use pileup()
hilbertvis
rsamtools
shortread
biostrings
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 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
7.9 years ago
phil.chapman
▴ 150
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 7.9 years ago by
Martin Morgan
25k • written 7.9 years ago by
phil.chapman
▴ 150
5
votes
7
replies
2.2k
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
8.1 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 8.3 years ago by
Martin Morgan
25k • written 8.3 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 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
steven.everman
▴ 10
0
votes
2
replies
1.4k
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 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
simonas.juzenas
▴ 10
1
vote
2
replies
2.2k
views
FastqSampler with trimmed paired-end reads
shortread
updated 3.1 years ago by
robmaz77
▴ 20 • written 8.7 years ago by
Arne Muller
▴ 20
1
vote
10
replies
2.9k
views
ShortRead with large fastq files
shortread
8.8 years ago
danova_fr
▴ 20
0
votes
4
replies
1.5k
views
gcContent error with shortread
shortread
8.9 years ago
danova_fr
▴ 20
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread
fastq
9.0 years ago • updated 8.9 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 9.0 years ago by
cookie
▴ 20
0
votes
2
replies
1.3k
views
ShortRead summary stats
shortread
illumina
9.0 years ago
danova_fr
▴ 20
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.0 years ago by
Martin Morgan
25k • written 9.0 years ago by
kelvinfrog75
• 0
5
votes
1
reply
3.1k
views
fastqSampler and writeFastq in shortread package
shortread
fastq
write
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
francesca.defilippis
▴ 100
0
votes
3
replies
2.7k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 9.2 years ago by
Valerie Obenchain
★ 6.8k • written 9.2 years ago by
newmanss
• 0
0
votes
3
replies
1.6k
views
Affect ShortRead readAligned behavior with ScanBamParam's reverseComplement parameter
shortread
readAligned
reverseComplement
ScanBamParam
9.2 years ago
jdavison
▴ 10
5
votes
5
replies
2.0k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics
chipseq
biomart
shortread
convert
biomaRt
9.5 years ago
patrick.schordert
▴ 30
0
votes
0
replies
950
views
Longest continuous sequence from multiple alignment
GO
ShortRead
GO
ShortRead
9.9 years ago
Guest User
★ 13k
50 results • Page
1 of 1
Recent ...
Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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