Showing : ShortRead • reset
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ShortRead qa() error: Error in density.default(qscore) : 'x' contains missing values
PROcess ShortRead PROcess ShortRead
updated 11.8 years ago by 25k • written 11.8 years ago by ▴ 300
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5
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2.0k
views
Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 300
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3
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2.5k
views
bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 12.5 years ago by ★ 8.2k • written 12.5 years ago by ▴ 680
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Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
12.6 years ago Noah Dowell ▴ 410
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3
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3.1k
views
Trouble creating a ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 410
0
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3
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7.2k
views
readFasta and gzipped FASTA files
ShortRead ShortRead
updated 12.6 years ago by 25k • written 12.6 years ago by ▴ 310
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3
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3.0k
views
readFastq, writeFastq, compressed files and unix pipes.
ShortRead ShortRead
updated 12.8 years ago by 25k • written 12.8 years ago by ▴ 310
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0
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990
views
readAligned with bowtie2 input
Alignment Cancer ShortRead Alignment Cancer ShortRead
12.8 years ago Martin Morgan 25k
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0
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979
views
readAligned with bowtie2 input
Alignment ShortRead Alignment ShortRead
12.8 years ago Maria Dermit ▴ 10
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2
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1.4k
views
FastqSampler sort by ID
ShortRead ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 390
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4
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1.2k
views
how to get the quality score system information from the reads
ShortRead ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ★ 2.0k
0
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1
reply
1.3k
views
trimTails function in ShortRead package give different results on the same input
Sequencing ShortRead Sequencing ShortRead
updated 12.9 years ago by 25k • written 12.9 years ago by ▴ 10
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1
reply
1.0k
views
how to plot quality report
ShortRead ShortRead
updated 13.1 years ago by 25k • written 13.1 years ago by ★ 2.0k
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votes
1
reply
1.0k
views
ShortRead package
ShortRead ShortRead
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 260
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1
reply
991
views
Cannot call ShortRead package FastqSampler from Linux
ShortRead ShortRead
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 10
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0
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838
views
report a possible bug of
Cancer ShortRead Cancer ShortRead
13.6 years ago Martin Morgan 25k
0
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1
reply
810
views
report a possible bug of
ShortRead ShortRead
updated 13.6 years ago by 25k • written 13.6 years ago by ★ 2.0k
0
votes
2
replies
2.1k
views
Rsamtools installation error
ShortRead Rsamtools ShortRead Rsamtools
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 60
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votes
1
reply
1.2k
views
remove empty short read after using trimEnds
ShortRead ShortRead
updated 13.8 years ago by 25k • written 13.8 years ago by ▴ 40
0
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11
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3.0k
views
NucleR: processReads/solveUserSEW0 - Error
IRanges ShortRead nucleR IRanges ShortRead nucleR
13.9 years ago Stefanie Ververs ▴ 70
0
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1
reply
1.3k
views
how to use writeFASTA
ShortRead ShortRead
updated 13.9 years ago by 25k • written 13.9 years ago by ★ 2.0k
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0
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1.3k
views
Problem when I install shortread
ShortRead ShortRead
14.0 years ago Wei Wu ▴ 10
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5
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1.9k
views
ShortRead error when reading BAM file
ShortRead ShortRead
updated 14.0 years ago by 25k • written 14.0 years ago by ▴ 650
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1
reply
1.4k
views
shortread readAligned with BWA
GO ShortRead GO ShortRead
updated 14.1 years ago by 25k • written 14.1 years ago by ▴ 280
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2
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1.5k
views
Error loading ShortRead
ShortRead ShortRead
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 500
0
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1
reply
1.2k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 14.7 years ago by 25k • written 14.7 years ago by ★ 8.2k
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1
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1.1k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 14.7 years ago by ★ 8.2k • written 14.7 years ago by ▴ 10
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2
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1.6k
views
mismatch & replacement
ShortRead ShortRead
updated 14.9 years ago by ▴ 590 • written 14.9 years ago by ▴ 90
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3
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1.5k
views
Problem installing Rsamtools and ShortRead under Fedora 10.
ShortRead Rsamtools ShortRead Rsamtools
updated 14.9 years ago by 6.7k • written 14.9 years ago by ▴ 50
0
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1
reply
1.2k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
updated 15.0 years ago by ★ 6.8k • written 15.0 years ago by ▴ 360
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1
reply
1.3k
views
ShortRead qa() for BAM files?
Coverage Alignment ShortRead Coverage Alignment ShortRead
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 260
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4
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1.7k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
15.0 years ago heyi xiao ▴ 360
0
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4
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1.5k
views
fastq upload time
ShortRead ShortRead
updated 15.0 years ago by 21k • written 15.0 years ago by ▴ 90
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3
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1.6k
views
ShortRead QA
Sequencing ShortRead Sequencing ShortRead
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 650
0
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3
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2.4k
views
Error installing Rsamtools
ShortRead Rsamtools ShortRead Rsamtools
updated 15.3 years ago by 25k • written 15.3 years ago by ★ 1.3k
0
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1
reply
1.2k
views
ShortRead information
ShortRead ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 10
0
votes
1
reply
926
views
Typo in ?FastqQuality help page?
ShortRead ShortRead
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 950
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2
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1.3k
views
ShortRead with BAM
ShortRead ShortRead
updated 15.4 years ago by 68k • written 15.4 years ago by ▴ 210
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1
reply
1.1k
views
Shortread and filtering of duplicate reads
ShortRead ShortRead
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 50
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2
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1.2k
views
ShortRead internal: too many 'snap' entries
ShortRead ShortRead
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 160
0
votes
1
reply
979
views
possible bug in extendReads() in package chipseq
Alignment ShortRead Alignment ShortRead
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 40
0
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2
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1.3k
views
pileup function in ShortRead package
Alignment ShortRead Alignment ShortRead
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 40
0
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5
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2.3k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.0 years ago by 25k • written 16.1 years ago by ▴ 40
0
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0
replies
1.1k
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
ShortRead charm ShortRead charm
16.5 years ago David Rossell ▴ 100
0
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1
reply
1.1k
views
Problems reading multiple MAQ map files with ShortRead ReadAligned
Cancer PROcess ShortRead charm Cancer PROcess ShortRead charm
16.5 years ago Martin Morgan 25k
0
votes
1
reply
932
views
Vignette for ShortRead
ShortRead ShortRead
updated 17.2 years ago by 25k • written 17.2 years ago by ▴ 330
96 results • Page 2 of 2
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Replies
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure by James W. MacDonald 68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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