Showing : zebrafish • reset
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1.6k
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 8.2 years ago by ★ 4.1k • written 8.2 years ago by ▴ 80
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1
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1.5k
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Importing and Extracting Annotation
annotation zebrafish probe
updated 8.6 years ago by 67k • written 8.6 years ago by • 0
9
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1
reply
2.5k
views
News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 9.5 years ago by ▴ 390 • written 9.5 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 10.2 years ago by 51k • written 10.2 years ago by ▴ 140
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0
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1.4k
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
10.3 years ago Thomas Maurel ▴ 800
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2
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2.0k
views
TxDb file for Drerio (ie zebrafish)
Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek
updated 10.7 years ago by 67k • written 10.7 years ago by ▴ 10
1
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1
reply
1.9k
views
Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 11.1 years ago by 67k • written 11.1 years ago by ▴ 80
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1
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1.4k
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ChIPpeakAnno, getAnnotation question
Annotation zebrafish convert biomaRt ChIPpeakAnno Annotation zebrafish convert biomaRt
updated 11.2 years ago by ★ 4.3k • written 11.2 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 11.2 years ago by ★ 4.3k • written 11.2 years ago by ★ 13k
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1
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1.1k
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affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 11.2 years ago by 67k • written 11.2 years ago by ▴ 80
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2
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1.4k
views
blast probe clusters when using Affymetrix Gene Array Strips
zebrafish zebrafish
updated 11.2 years ago by 67k • written 11.2 years ago by ▴ 80
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0
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1.6k
views
Useful information about Ensembl release 71 mart databases
zebrafish PolyPhen SIFT affy genomes zebrafish PolyPhen SIFT affy genomes
11.6 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
11.8 years ago florian.hahne@novartis.com ★ 1.6k
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2
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1.9k
views
Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt zebrafish biomaRt
updated 11.8 years ago by ★ 1.6k • written 11.8 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 12.2 years ago by ▴ 100 • written 12.2 years ago by ▴ 140
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1
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1.6k
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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
12.5 years ago Thomas Maurel ▴ 800
0
votes
9
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2.0k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 13.7 years ago by 21k • written 13.7 years ago by 16k
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3
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1.8k
views
Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 13.7 years ago by 21k • written 13.7 years ago by ▴ 140
0
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0
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1.1k
views
Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
14.1 years ago Neel Aluru ▴ 460
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0
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1.2k
views
Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
14.1 years ago Neel Aluru ▴ 460
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1
reply
1.3k
views
Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 14.3 years ago by ★ 7.2k • written 14.3 years ago by ▴ 40
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1
reply
1.2k
views
Annotation in Agi4x44PreProcess
Annotation zebrafish probe Agi4x44PreProcess Annotation zebrafish probe Agi4x44PreProcess
updated 14.3 years ago by ★ 7.2k • written 14.3 years ago by ▴ 40
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0
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1.5k
views
AgiMicroRna - FilterMicroRna and SignificantMicroRna function
miRNA zebrafish probe AgiMicroRna miRNA zebrafish probe AgiMicroRna
14.5 years ago Neel Aluru ▴ 460
0
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1
reply
1.1k
views
GOstats - zebrafish
Annotation GO zebrafish probe Annotation GO zebrafish probe
updated 14.5 years ago by 67k • written 14.5 years ago by ▴ 460
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0
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1.2k
views
Ensembl mart release 57: Useful information
SNP GO Homo sapiens zebrafish SNP GO Homo sapiens zebrafish
14.7 years ago Rhoda Kinsella ▴ 660
0
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6
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1.2k
views
annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 14.8 years ago by 67k • written 14.8 years ago by ★ 1.5k
0
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1
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801
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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 14.8 years ago by ★ 2.0k • written 14.8 years ago by ★ 2.0k
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5
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1.5k
views
Agilent zebrafish4x44 database
zebrafish zebrafish
updated 15.0 years ago by ★ 1.3k • written 15.0 years ago by ▴ 460
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0
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887
views
Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
15.3 years ago Hervé Pagès 16k
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1
reply
940
views
siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
15.4 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
15.5 years ago Georg Otto ▴ 510
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0
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1.0k
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.5 years ago Rhoda Kinsella ▴ 660
0
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0
replies
982
views
JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.6 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 15.7 years ago by ★ 6.5k • written 15.7 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 15.9 years ago by 67k • written 15.9 years ago by ▴ 300
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1
reply
883
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 16.2 years ago by ★ 7.2k • written 16.2 years ago by ▴ 60
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2
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1.6k
views
agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.6 years ago Georg Otto ▴ 510
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0
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945
views
homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
17.2 years ago Mayte Suarez-Farinas ▴ 510
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2
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1.1k
views
simpleaffy QCstats and affyQAReport repost
zebrafish probe affy zebrafish probe affy
updated 17.3 years ago by ★ 1.1k • written 17.3 years ago by ▴ 70
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votes
3
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1.3k
views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 17.5 years ago by ★ 7.4k • written 17.5 years ago by ▴ 160
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0
replies
903
views
agilent zebrafish array annotation package
zebrafish zebrafish
18.9 years ago Georg Otto ▴ 510
0
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1
reply
1.3k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 19.2 years ago by ▴ 420 • written 19.2 years ago by ▴ 150
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0
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1.4k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
19.3 years ago Steffen Durinck ▴ 420
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votes
0
replies
1.2k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
19.3 years ago Georg Otto ▴ 510
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votes
2
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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 19.3 years ago by ▴ 780 • written 19.3 years ago by ★ 1.4k
0
votes
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 19.3 years ago by ★ 1.4k • written 19.3 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 19.5 years ago by ★ 2.9k • written 19.5 years ago by ▴ 510
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0
replies
893
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
20.1 years ago Crispin Miller ★ 1.1k
0
votes
1
reply
861
views
problems using cdfenv
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
updated 20.1 years ago by 67k • written 20.1 years ago by ▴ 510
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1
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818
views
affymetrix zebrafish chip
zebrafish zebrafish
updated 20.4 years ago by 67k • written 20.4 years ago by ▴ 140
50 results • Page 1 of 1
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Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Votes
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Awards • All
Popular Question to prabin.dm • 0
Popular Question to Robert Castelo ★ 3.4k
Popular Question to Michael Stadler ▴ 350
Scholar to ATpoint ★ 4.5k
Commentator to James W. MacDonald 67k
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