Showing : ShortRead • reset
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 ▴ 240 • written 6.0 years ago by ▴ 60
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 5.1 years ago by ▴ 60 • written 5.1 years ago by ▴ 60
5
votes
1
reply
3.2k
views
fastqSampler and writeFastq in shortread package
shortread fastq write
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 100
5
votes
1
reply
3.3k
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
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
5
votes
4
replies
3.2k
views
Trimming with ShortRead
shortread
updated 9.1 years ago by 25k • written 9.1 years ago by ▴ 20
5
votes
7
replies
2.3k
views
Using ShortRead (or other) to trim from pattern match onwards
shortread
updated 8.1 years ago by 25k • written 8.1 years ago by ▴ 20
5
votes
4
replies
2.7k
views
strsplit method for DNAStringSet objects
biostrings shortread
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 70
4
votes
7
replies
2.1k
views
IRanges/ShortRead causing crash?
iranges shortread Biostrings
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 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 25k • written 6.2 years ago by ▴ 50
4
votes
7
replies
2.0k
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
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 ★ 1.5k • written 6.2 years ago by ▴ 10
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 7.4 years ago by 65k • written 7.4 years ago by ▴ 20
2
votes
3
replies
1.6k
views
Running old packages on Mac
ShortRead
written 3.2 years ago by ▴ 90
2
votes
5
replies
1.8k
views
ShortRead trim sequence at specific position
shortread fastq
9.1 years ago • updated 9.0 years ago danova_fr ▴ 20
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 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 25k • written 8.7 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Shortread convert S4 vector qualityScore to vector
shortread
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 90
1
vote
2
replies
1.2k
views
FastqStreamer and qualitytype
shortread
7.7 years ago David ▴ 860
1
vote
10
replies
3.0k
views
ShortRead with large fastq files
shortread
8.9 years ago danova_fr ▴ 20
1
vote
2
replies
1.5k
views
Reading fastq file after narrowing sequences
ShortRead FastqStreamer
6.4 years ago ioannis.vardaxis ▴ 30
1
vote
2
replies
1.2k
views
bplapply with ShortRead functions
shortread biocparallel
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 100
1
vote
2
replies
2.2k
views
FastqSampler with trimmed paired-end reads
shortread
updated 3.2 years ago by ▴ 20 • written 8.8 years ago by ▴ 20
1
vote
2
replies
1.7k
views
ShortRead quality assessment functions (qa and qa2) from ShortReadQ object
shortread
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 150
1
vote
3
replies
1.4k
views
Remove reads from raw fastq
shortread biostrings
updated 5.5 years ago by 50k • written 5.5 years ago by • 0
1
vote
1
reply
1.0k
views
error: incorrect number of fields (1) input.bam:1
shortread readaligned
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina shortread
updated 9.1 years ago by 25k • written 9.1 years ago by • 0
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 25k • written 8.4 years ago by ▴ 10
1
vote
3
replies
842
views
support for reading direct RNA-Seq FASTQs
ShortRead nanopore
2.0 years ago kent.riemondy ▴ 20
1
vote
1
reply
860
views
Unable to install "scruff" with BiocManager::install()
scruff Install ShortRead
updated 20 months ago by 3.8k • written 20 months ago by • 0
0
votes
1
reply
1.0k
views
remove empty short read after using trimEnds
ShortRead ShortRead
updated 12.4 years ago by 25k • written 12.4 years ago by ▴ 40
0
votes
2
replies
1.7k
views
Rsamtools installation error
ShortRead Rsamtools ShortRead Rsamtools
updated 12.2 years ago by 25k • written 12.2 years ago by ▴ 60
0
votes
1
reply
643
views
report a possible bug of
ShortRead ShortRead
updated 12.2 years ago by 25k • written 12.2 years ago by ★ 2.0k
0
votes
0
replies
697
views
report a possible bug of
Cancer ShortRead Cancer ShortRead
12.2 years ago Martin Morgan 25k
0
votes
1
reply
766
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 10
0
votes
1
reply
828
views
ShortRead package
ShortRead ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 260
0
votes
1
reply
827
views
how to plot quality report
ShortRead ShortRead
updated 11.7 years ago by 25k • written 11.7 years ago by ★ 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 25k • written 11.5 years ago by ▴ 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 25k • written 11.5 years ago by ★ 2.0k
0
votes
0
replies
810
views
readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
11.4 years ago Maria Dermit ▴ 10
0
votes
3
replies
2.5k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 11.4 years ago by 25k • written 11.4 years ago by ▴ 310
0
votes
3
replies
6.0k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 11.2 years ago by 25k • written 11.2 years ago by ▴ 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 25k • written 11.2 years ago by ▴ 410
0
votes
0
replies
1.1k
views
Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
11.2 years ago Noah Dowell ▴ 410
0
votes
3
replies
2.2k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 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 ★ 6.8k • written 10.7 years ago by ▴ 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 25k • written 10.4 years ago by ▴ 300
0
votes
0
replies
976
views
Longest continuous sequence from multiple alignment
GO ShortRead GO ShortRead
10.0 years ago Guest User ★ 13k
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
0
votes
3
replies
2.7k
views
ShortRead- how to edit the id in a fastq
ShortRead
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by • 0
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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