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CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
9.8 years ago Julie Zhu ★ 4.3k
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2
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Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
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6
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separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
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GWASTools suggestions: explicit interface for GenotypeReaders,
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updated 10.4 years ago by ▴ 870 • written 10.4 years ago by ▴ 70
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923
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SAM for protemics - low q values
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10.6 years ago Hendrik Nolte ▴ 10
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4
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DEXSeq on two-exon genes: how to specify a formula without redundant terms
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11.0 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
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BitSeq: Required input for 3' bias correction on transcripts.
Transcription RNASeq safe BitSeq Transcription RNASeq safe BitSeq
11.3 years ago Peter Glaus ▴ 70
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Log transformation and left censoring
limma safe edgeR limma safe edgeR
11.3 years ago Paul Harrison ▴ 100
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BitSeq: Required input for 3' bias correction on transcripts.
RNASeq safe BitSeq RNASeq safe BitSeq
11.3 years ago Dave Gerrard ▴ 40
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frma for Nimblegen arrays?
Microarray Annotation Normalization affy PROcess safe frma frmaTools Microarray affy
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ▴ 260
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SCAN UPC probability - validation of gene expression results using UPC
hgu133a2 safe SCAN.UPC hgu133a2 safe SCAN.UPC
updated 11.5 years ago by ▴ 590 • written 11.5 years ago by ▴ 850
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SCAN UPC probability - validation of gene expression results using UPC
hgu133a2 safe hgu133a2 safe
11.5 years ago Guest User ★ 13k
0
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5
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1.4k
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frma for Nimblegen arrays?
Microarray Normalization affy PROcess safe frma Microarray Normalization affy PROcess
updated 11.5 years ago by ▴ 830 • written 11.5 years ago by ▴ 260
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0
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flowCore 1.22.0 broken for some FCS files
Cancer safe flowCore Cancer safe flowCore
11.9 years ago Josef Spidlen ▴ 140
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1.2k
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dbSNP strand information
SNPlocs safe SNPlocs safe
12.2 years ago Alex Gutteridge ▴ 650
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3
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1.5k
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Strand information for dbSNP packages
SNPlocs safe SNPlocs safe
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 650
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Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
safe BiocInstaller safe BiocInstaller
12.4 years ago Firas Swidan ▴ 50
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Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
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12.4 years ago Andrea Grilli ▴ 240
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Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
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updated 12.4 years ago by ★ 8.2k • written 12.4 years ago by ▴ 50
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1
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Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
updated 12.8 years ago by ▴ 590 • written 12.8 years ago by ★ 2.3k
0
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5
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1.6k
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Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 13.0 years ago by ★ 3.6k • written 13.0 years ago by ▴ 220
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0
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1.0k
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Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
13.0 years ago Harris A. Jaffee ▴ 590
0
votes
0
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880
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Can't reproduce assessment data included in affycomp package
Cancer affycomp PROcess safe Cancer affycomp PROcess safe
13.1 years ago Philippe Serhal ▴ 10
0
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1
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1.5k
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Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 13.1 years ago by ★ 3.6k • written 13.1 years ago by ▴ 220
0
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4
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4.4k
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Bioconductor with Affymetrix Mouse Gene 1.0 ST
Annotation cdf PROcess safe Annotation cdf PROcess safe
13.1 years ago M. Emily Merrill ▴ 20
0
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3
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1.1k
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Package xps - Problem accessing README file
safe xps safe xps
updated 13.5 years ago by ★ 3.9k • written 13.5 years ago by ★ 8.2k
0
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0
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670
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Now you can smoke anywhere you want!
Cancer safe Cancer safe
14.7 years ago inLife E-Cigarettes ▴ 10
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660
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You Don't Have to Quit Smoking. New Technology!
Cancer safe Cancer safe
14.7 years ago inLife E-Cigarettes ▴ 10
0
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0
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778
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biomaRt - current devel version of biomaRt+RCurl don't work
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14.9 years ago Patrick Aboyoun ★ 1.6k
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774
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RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'
Cancer RdbiPgSQL safe Cancer RdbiPgSQL safe
15.0 years ago Ben Madin ▴ 20
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2
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909
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RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'
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updated 15.0 years ago by 16k • written 15.0 years ago by ▴ 20
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0
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655
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!SPAM: Sale Offer:- ViagraCializ Pills at LowestPrices on net! $1.31/tab, find out more ewlelk 6qu
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15.4 years ago Anisa Gracie ▴ 10
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1
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2.0k
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Important information (Discover The Ways That We Protect Your Online Access)
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15.9 years ago �2008 HALIFAX SECURITY ▴ 20
0
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4
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1.5k
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About beadarray normaliseIllumina() warning messages
Normalization GO safe beadarray lumi Normalization GO safe beadarray lumi
updated 16.3 years ago by ▴ 410 • written 16.3 years ago by ▴ 150
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1
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1.3k
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[R] Why SAM has totally diffent results in R2.1.1 and R2.4.0
Microarray Genetics Survival multtest siggenes safe Microarray Genetics Survival multtest
updated 17.5 years ago by ▴ 900 • written 17.5 years ago by 25k
0
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2
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1.6k
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BH vs BY in p.adjust
Coverage limma safe Coverage limma safe
updated 17.8 years ago by ★ 13k • written 17.8 years ago by ▴ 50
0
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5
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1.3k
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Missing chromosomal locations in hgu133a package
hgu133a AnnBuilder safe hgu133a AnnBuilder safe
updated 17.8 years ago by ▴ 870 • written 17.8 years ago by ▴ 60
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1
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1.1k
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limma 3-way interaction
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18.0 years ago Jacob Michaelson ▴ 320
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6
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1.1k
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Limma: background correction. Use or ignore?
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updated 18.1 years ago by ★ 2.4k • written 18.1 years ago by ★ 1.9k
0
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2
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1.2k
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GeneSpring can call R functions?
GO GeneSpring safe GO GeneSpring safe
updated 19.0 years ago by ★ 1.1k • written 19.0 years ago by ▴ 250
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2
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1.1k
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trouble with yeastann function in AnnBuilder
Annotation Yeast probe AnnBuilder safe Annotation Yeast probe AnnBuilder safe
updated 19.3 years ago by ▴ 10 • written 19.3 years ago by ▴ 320
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2
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1.3k
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Bioconductor data sets - Unigene IDs
probe safe probe safe
updated 21.6 years ago by ★ 2.3k • written 21.6 years ago by ★ 13k
42 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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