Showing : zebrafish • reset
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2.9k
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goseq/nullp with non-native identifiers
Annotation GO zebrafish goseq Annotation GO zebrafish goseq
updated 11.7 years ago by ▴ 100 • written 11.7 years ago by ▴ 140
9
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1
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2.2k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 9.0 years ago by ▴ 390 • written 9.0 years ago by ▴ 800
0
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9
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1.9k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 13.2 years ago by 21k • written 13.2 years ago by 16k
1
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1
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1.8k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 80
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2
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1.8k
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TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 10.2 years ago by 65k • written 10.2 years ago by ▴ 10
0
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2
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1.8k
views
Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt zebrafish biomaRt
updated 11.3 years ago by ★ 1.6k • written 11.3 years ago by ★ 13k
0
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3
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1.7k
views
Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 13.2 years ago by 21k • written 13.2 years ago by ▴ 140
0
votes
2
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1.6k
views
Help with loading newly created custom annotation db into R session
Annotation GO GUI zebrafish probe Annotation GO GUI zebrafish probe
updated 15.3 years ago by 65k • written 15.3 years ago by ▴ 300
0
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0
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1.5k
views
Useful information about Ensembl release 71 mart databases
zebrafish PolyPhen SIFT affy genomes zebrafish PolyPhen SIFT affy genomes
11.1 years ago Thomas Maurel ▴ 800
0
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2
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1.5k
views
agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.1 years ago Georg Otto ▴ 510
0
votes
2
replies
1.4k
views
Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 7.6 years ago by ★ 3.9k • written 7.7 years ago by ▴ 70
0
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1
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1.4k
views
Useful information about Ensembl release 67 mart databases
miRNA GO Caenorhabditis elegans Sus scrofa zebrafish PolyPhen SIFT miRNA GO Sus scrofa
12.0 years ago Thomas Maurel ▴ 800
0
votes
0
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1.4k
views
AgiMicroRna - FilterMicroRna and SignificantMicroRna function
miRNA zebrafish probe AgiMicroRna miRNA zebrafish probe AgiMicroRna
14.0 years ago Neel Aluru ▴ 460
0
votes
1
reply
1.4k
views
Group-wise gcrma normalization
Microarray Normalization Clustering zebrafish probe gcrma Microarray Normalization probe
updated 15.2 years ago by ★ 6.5k • written 15.2 years ago by ▴ 30
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1
reply
1.3k
views
ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 10.6 years ago by ★ 4.3k • written 10.6 years ago by ★ 13k
0
votes
1
reply
1.3k
views
ChIPpeakAnno, getAnnotation question
Annotation zebrafish convert biomaRt ChIPpeakAnno Annotation zebrafish convert biomaRt
updated 10.6 years ago by ★ 4.3k • written 10.6 years ago by ▴ 10
0
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5
replies
1.3k
views
Agilent zebrafish4x44 database
zebrafish zebrafish
updated 14.5 years ago by ★ 1.3k • written 14.5 years ago by ▴ 460
0
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1
reply
1.3k
views
Importing and Extracting Annotation
annotation zebrafish probe
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
0
votes
0
replies
1.3k
views
Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt ideogram genomes zebrafish biomaRt ideogram genomes
11.2 years ago florian.hahne@novartis.com ★ 1.6k
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2
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1.3k
views
blast probe clusters when using Affymetrix Gene Array Strips
zebrafish zebrafish
updated 10.7 years ago by 65k • written 10.7 years ago by ▴ 80
0
votes
0
replies
1.3k
views
Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
9.7 years ago Thomas Maurel ▴ 800
0
votes
1
reply
1.2k
views
zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 18.8 years ago by ★ 1.4k • written 18.8 years ago by ★ 1.1k
0
votes
0
replies
1.2k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Steffen Durinck ▴ 420
0
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1
reply
1.2k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 18.6 years ago by ▴ 420 • written 18.6 years ago by ▴ 150
0
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3
replies
1.2k
views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 160
0
votes
2
replies
1.1k
views
Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 9.7 years ago by 50k • written 9.7 years ago by ▴ 140
0
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1
reply
1.1k
views
Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 13.8 years ago by ★ 7.2k • written 13.8 years ago by ▴ 40
0
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0
replies
1.1k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Georg Otto ▴ 510
0
votes
0
replies
1.1k
views
Ensembl mart release 57: Useful information
SNP GO Homo sapiens zebrafish SNP GO Homo sapiens zebrafish
14.2 years ago Rhoda Kinsella ▴ 660
0
votes
1
reply
1.1k
views
Annotation in Agi4x44PreProcess
Annotation zebrafish probe Agi4x44PreProcess Annotation zebrafish probe Agi4x44PreProcess
updated 13.8 years ago by ★ 7.2k • written 13.8 years ago by ▴ 40
0
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4
replies
1.1k
views
Error in AnnBuilder writeAnnData2Pkg
Annotation zebrafish AnnBuilder Annotation zebrafish AnnBuilder
updated 19.0 years ago by ★ 2.9k • written 19.0 years ago by ▴ 510
0
votes
2
replies
1.1k
views
zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 18.8 years ago by ▴ 780 • written 18.8 years ago by ★ 1.4k
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6
replies
1.1k
views
annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 14.2 years ago by 65k • written 14.2 years ago by ★ 1.5k
0
votes
0
replies
1.1k
views
Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
13.6 years ago Neel Aluru ▴ 460
0
votes
1
reply
1.0k
views
affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 80
0
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2
replies
994
views
simpleaffy QCstats and affyQAReport repost
zebrafish probe affy zebrafish probe affy
updated 16.8 years ago by ★ 1.1k • written 16.8 years ago by ▴ 70
0
votes
0
replies
983
views
Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
13.6 years ago Neel Aluru ▴ 460
0
votes
1
reply
962
views
Invalid "marrayInfo" object
zebrafish zebrafish
updated 20.8 years ago by ▴ 920 • written 20.8 years ago by ▴ 230
0
votes
1
reply
954
views
GOstats - zebrafish
Annotation GO zebrafish probe Annotation GO zebrafish probe
updated 14.0 years ago by 65k • written 14.0 years ago by ▴ 460
0
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0
replies
953
views
problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
15.0 years ago Georg Otto ▴ 510
0
votes
0
replies
931
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
0
votes
0
replies
889
views
Re: lm.series, design matrix
zebrafish limma zebrafish limma
20.8 years ago James Wettenhall ▴ 1000
0
votes
0
replies
860
views
JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.0 years ago Moshe Pritsker, Editor, JoVE ▴ 20
0
votes
1
reply
842
views
siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
14.9 years ago Bio Sam ▴ 60
0
votes
0
replies
840
views
homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
16.6 years ago Mayte Suarez-Farinas ▴ 510
0
votes
0
replies
838
views
agilent zebrafish array annotation package
zebrafish zebrafish
18.3 years ago Georg Otto ▴ 510
0
votes
0
replies
828
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
19.6 years ago Crispin Miller ★ 1.1k
0
votes
0
replies
809
views
Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
14.8 years ago Hervé Pagès 16k
0
votes
1
reply
802
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 15.6 years ago by ★ 7.2k • written 15.6 years ago by ▴ 60
0
votes
1
reply
765
views
problems using cdfenv
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
updated 19.6 years ago by 65k • written 19.6 years ago by ▴ 510
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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