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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1.9k
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Finding my un-counted reads
Sequencing rtracklayer ShortRead GenomicRanges Sequencing rtracklayer ShortRead
updated 12.0 years ago by ★ 6.8k • written 12.0 years ago by ▴ 300
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3
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2.5k
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bioc package installation problem
ShortRead BiocInstaller ShortRead BiocInstaller
updated 12.4 years ago by ★ 8.2k • written 12.4 years ago by ▴ 680
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Sorry for cross post: Trouble creating ShortReadQ object and using writeFastq
Preprocessing ShortRead Preprocessing ShortRead
12.5 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 12.5 years ago by 25k • written 12.5 years ago by ▴ 410
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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 12.7 years ago by 25k • written 12.7 years ago by ▴ 310
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0
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989
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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977
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 12.8 years ago by 25k • written 12.8 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 12.8 years ago by 25k • written 12.8 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
0
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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votes
1
reply
987
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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834
views
report a possible bug of
Cancer ShortRead Cancer ShortRead
13.5 years ago Martin Morgan 25k
0
votes
1
reply
804
views
report a possible bug of
ShortRead ShortRead
updated 13.5 years ago by 25k • written 13.5 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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1
reply
1.2k
views
remove empty short read after using trimEnds
ShortRead ShortRead
updated 13.7 years ago by 25k • written 13.7 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
13.8 years ago Stefanie Ververs ▴ 70
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1
reply
1.3k
views
how to use writeFASTA
ShortRead ShortRead
updated 13.8 years ago by 25k • written 13.8 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
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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 14.3 years ago by 25k • written 14.3 years ago by ▴ 500
0
votes
1
reply
1.2k
views
A question about ShortRead_1.8.2.tar.gz.
ShortRead ShortRead
updated 14.6 years ago by 25k • written 14.6 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 14.6 years ago by ★ 8.2k • written 14.6 years ago by ▴ 10
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2
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1.6k
views
mismatch & replacement
ShortRead ShortRead
updated 14.8 years ago by ▴ 590 • written 14.8 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
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1
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1.2k
views
ShortRead for sequencing data quality assessment
Sequencing ShortRead Sequencing ShortRead
updated 14.9 years ago by ★ 6.8k • written 14.9 years ago by ▴ 360
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1
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1.3k
views
ShortRead qa() for BAM files?
Coverage Alignment ShortRead Coverage Alignment ShortRead
updated 14.9 years ago by 25k • written 14.9 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
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votes
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 15.1 years ago by 25k • written 15.1 years ago by ▴ 650
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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
918
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
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1.1k
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Shortread and filtering of duplicate reads
ShortRead ShortRead
updated 15.6 years ago by 25k • written 15.6 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
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1
reply
971
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 15.9 years ago by 25k • written 15.9 years ago by ▴ 40
0
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5
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2.2k
views
read coverage per transcript for RNASeq
RNASeq Coverage PROcess ShortRead RNASeq Coverage PROcess ShortRead
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 40
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0
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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
925
views
Vignette for ShortRead
ShortRead ShortRead
updated 17.1 years ago by 25k • written 17.1 years ago by ▴ 330
96 results • Page 2 of 2
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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