Showing : zebrafish • reset
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 8.5 years ago by ★ 4.1k • written 8.5 years ago by ▴ 80
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1
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1.6k
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Importing and Extracting Annotation
annotation zebrafish probe
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
9
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1
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2.5k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 9.8 years ago by ▴ 390 • written 9.8 years ago by ▴ 800
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2
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1.3k
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Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 10.5 years ago by 52k • written 10.5 years ago by ▴ 140
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1.4k
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
10.6 years ago Thomas Maurel ▴ 800
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2
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2.1k
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TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 10
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1
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2.0k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 11.4 years ago by 68k • written 11.4 years ago by ▴ 80
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1
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1.5k
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ChIPpeakAnno, getAnnotation question
Annotation zebrafish convert biomaRt ChIPpeakAnno Annotation zebrafish convert biomaRt
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ▴ 10
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1
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1.5k
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ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ★ 13k
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1
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1.2k
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affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 11.5 years ago by 68k • written 11.5 years ago by ▴ 80
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2
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1.4k
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blast probe clusters when using Affymetrix Gene Array Strips
zebrafish zebrafish
updated 11.5 years ago by 68k • written 11.5 years ago by ▴ 80
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0
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1.7k
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Useful information about Ensembl release 71 mart databases
zebrafish PolyPhen SIFT affy genomes zebrafish PolyPhen SIFT affy genomes
11.9 years ago Thomas Maurel ▴ 800
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0
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1.4k
views
Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt ideogram genomes zebrafish biomaRt ideogram genomes
12.1 years ago florian.hahne@novartis.com ★ 1.6k
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2.0k
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Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt zebrafish biomaRt
updated 12.1 years ago by ★ 1.6k • written 12.1 years ago by ★ 13k
1
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1
reply
3.2k
views
goseq/nullp with non-native identifiers
Annotation GO zebrafish goseq Annotation GO zebrafish goseq
updated 12.5 years ago by ▴ 100 • written 12.5 years ago by ▴ 140
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1
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1.7k
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Useful information about Ensembl release 67 mart databases
miRNA GO Caenorhabditis elegans Sus scrofa zebrafish PolyPhen SIFT miRNA GO Sus scrofa
12.8 years ago Thomas Maurel ▴ 800
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9
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2.1k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.0 years ago by 21k • written 14.0 years ago by 16k
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3
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1.9k
views
Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 14.0 years ago by 21k • written 14.0 years ago by ▴ 140
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1.2k
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Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
14.4 years ago Neel Aluru ▴ 460
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0
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1.3k
views
Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
14.4 years ago Neel Aluru ▴ 460
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1
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1.3k
views
Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 40
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1
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1.3k
views
Annotation in Agi4x44PreProcess
Annotation zebrafish probe Agi4x44PreProcess Annotation zebrafish probe Agi4x44PreProcess
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 40
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0
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1.6k
views
AgiMicroRna - FilterMicroRna and SignificantMicroRna function
miRNA zebrafish probe AgiMicroRna miRNA zebrafish probe AgiMicroRna
14.8 years ago Neel Aluru ▴ 460
0
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1
reply
1.2k
views
GOstats - zebrafish
Annotation GO zebrafish probe Annotation GO zebrafish probe
updated 14.8 years ago by 68k • written 14.8 years ago by ▴ 460
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0
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1.3k
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Ensembl mart release 57: Useful information
SNP GO Homo sapiens zebrafish SNP GO Homo sapiens zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
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6
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1.3k
views
annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 15.1 years ago by 68k • written 15.1 years ago by ★ 1.5k
0
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1
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840
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GOstats testing using EntrezGene IDs not in chip-specific annotation package?
GO zebrafish probe affy GOstats AnnotationDbi GO zebrafish probe affy GOstats
updated 15.1 years ago by ★ 2.0k • written 15.1 years ago by ★ 2.0k
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5
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1.6k
views
Agilent zebrafish4x44 database
zebrafish zebrafish
updated 15.3 years ago by ★ 1.3k • written 15.3 years ago by ▴ 460
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0
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929
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Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
15.6 years ago Hervé Pagès 16k
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1
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977
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siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
15.7 years ago Bio Sam ▴ 60
0
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0
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1.1k
views
problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
15.8 years ago Georg Otto ▴ 510
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0
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1.1k
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.8 years ago Rhoda Kinsella ▴ 660
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0
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1.0k
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JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.9 years ago Moshe Pritsker, Editor, JoVE ▴ 20
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1
reply
1.5k
views
Group-wise gcrma normalization
Microarray Normalization Clustering zebrafish probe gcrma Microarray Normalization probe
updated 16.0 years ago by ★ 6.5k • written 16.0 years ago by ▴ 30
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2
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1.8k
views
Help with loading newly created custom annotation db into R session
Annotation GO GUI zebrafish probe Annotation GO GUI zebrafish probe
updated 16.2 years ago by 68k • written 16.2 years ago by ▴ 300
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1
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922
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 16.5 years ago by ★ 7.2k • written 16.5 years ago by ▴ 60
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2
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1.7k
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agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.9 years ago Georg Otto ▴ 510
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0
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1000
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homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
17.5 years ago Mayte Suarez-Farinas ▴ 510
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1.2k
views
simpleaffy QCstats and affyQAReport repost
zebrafish probe affy zebrafish probe affy
updated 17.6 years ago by ★ 1.1k • written 17.6 years ago by ▴ 70
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3
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1.4k
views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 17.8 years ago by ★ 7.4k • written 17.8 years ago by ▴ 160
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0
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937
views
agilent zebrafish array annotation package
zebrafish zebrafish
19.2 years ago Georg Otto ▴ 510
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1
reply
1.4k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 19.5 years ago by ▴ 420 • written 19.5 years ago by ▴ 150
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0
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1.4k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
19.6 years ago Steffen Durinck ▴ 420
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0
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1.3k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
19.6 years ago Georg Otto ▴ 510
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2
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1.3k
views
zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 19.6 years ago by ▴ 780 • written 19.6 years ago by ★ 1.4k
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1
reply
1.4k
views
zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 19.6 years ago by ★ 1.4k • written 19.6 years ago by ★ 1.1k
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4
replies
1.3k
views
Error in AnnBuilder writeAnnData2Pkg
Annotation zebrafish AnnBuilder Annotation zebrafish AnnBuilder
updated 19.8 years ago by ★ 2.9k • written 19.8 years ago by ▴ 510
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0
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934
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
20.4 years ago Crispin Miller ★ 1.1k
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votes
1
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899
views
problems using cdfenv
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
updated 20.4 years ago by 68k • written 20.4 years ago by ▴ 510
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1
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851
views
affymetrix zebrafish chip
zebrafish zebrafish
updated 20.7 years ago by 68k • written 20.7 years ago by ▴ 140
50 results • Page 1 of 1
Recent ...
Replies
Comment: DepMap data mismatch by Laurent Gatto 1.6k
It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…
Comment: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
If you are using `conumee2`, then you are in the wrong place. That isn't a Bioconductor package (yet? No idea if they have/will submit it).
Answer: myvariant error by James W. MacDonald 68k
You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…
Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?
Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Awards • All
Popular Question to Laurent Gatto 1.6k
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Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
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