Showing : zebrafish • reset
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 8.6 years ago by ★ 4.1k • written 8.6 years ago by ▴ 80
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Importing and Extracting Annotation
annotation zebrafish probe
updated 9.0 years ago by 68k • written 9.0 years ago by • 0
9
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2.5k
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News: Ensembl release 80 is out!
biomart Ensembl zebrafish Rat 1000 genomes phase 3 News
updated 9.9 years ago by ▴ 390 • written 9.9 years ago by ▴ 800
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Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 10.6 years ago by 52k • written 10.6 years ago by ▴ 140
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
10.7 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 11.1 years ago by 68k • written 11.1 years ago by ▴ 10
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Mapping Affymetrix annotations with Bioconductor annotations
Annotation Organism zebrafish cdf affy AnnotationForge Annotation Organism zebrafish cdf
updated 11.5 years ago by 68k • written 11.5 years ago by ▴ 80
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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 11.6 years ago by ▴ 10
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ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 11.6 years ago by ★ 4.3k • written 11.6 years ago by ★ 13k
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1.2k
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affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 11.6 years ago by 68k • written 11.6 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 11.6 years ago by 68k • written 11.6 years ago by ▴ 80
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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
12.0 years ago Thomas Maurel ▴ 800
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1.5k
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Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt ideogram genomes zebrafish biomaRt ideogram genomes
12.2 years ago florian.hahne@novartis.com ★ 1.6k
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Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt zebrafish biomaRt
updated 12.2 years ago by ★ 1.6k • written 12.2 years ago by ★ 13k
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goseq/nullp with non-native identifiers
Annotation GO zebrafish goseq Annotation GO zebrafish goseq
updated 12.6 years ago by ▴ 100 • written 12.6 years ago by ▴ 140
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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
12.9 years ago Thomas Maurel ▴ 800
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9
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2.2k
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Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.1 years ago by 21k • written 14.1 years ago by 16k
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3
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1.9k
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Mapping microarray probes to the genome using findOverlaps
Alignment Annotation zebrafish probe Alignment Annotation zebrafish probe
updated 14.1 years ago by 21k • written 14.1 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
14.5 years ago Neel Aluru ▴ 460
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1.3k
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Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
14.5 years ago Neel Aluru ▴ 460
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1
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1.4k
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Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ▴ 40
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1.3k
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Annotation in Agi4x44PreProcess
Annotation zebrafish probe Agi4x44PreProcess Annotation zebrafish probe Agi4x44PreProcess
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ▴ 40
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1.6k
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AgiMicroRna - FilterMicroRna and SignificantMicroRna function
miRNA zebrafish probe AgiMicroRna miRNA zebrafish probe AgiMicroRna
14.9 years ago Neel Aluru ▴ 460
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1
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1.2k
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GOstats - zebrafish
Annotation GO zebrafish probe Annotation GO zebrafish probe
updated 14.9 years ago by 68k • written 14.9 years ago by ▴ 460
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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
15.1 years ago Rhoda Kinsella ▴ 660
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6
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1.3k
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annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 15.2 years ago by 68k • written 15.2 years ago by ★ 1.5k
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853
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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 15.2 years ago by ★ 2.0k • written 15.2 years ago by ★ 2.0k
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5
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1.6k
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Agilent zebrafish4x44 database
zebrafish zebrafish
updated 15.4 years ago by ★ 1.3k • written 15.4 years ago by ▴ 460
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937
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Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
15.7 years ago Hervé Pagès 16k
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991
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siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
15.8 years ago Bio Sam ▴ 60
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1.1k
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problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
15.9 years ago Georg Otto ▴ 510
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1.1k
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Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.9 years ago Rhoda Kinsella ▴ 660
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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
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1.5k
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Group-wise gcrma normalization
Microarray Normalization Clustering zebrafish probe gcrma Microarray Normalization probe
updated 16.1 years ago by ★ 6.5k • written 16.1 years ago by ▴ 30
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1.8k
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Help with loading newly created custom annotation db into R session
Annotation GO GUI zebrafish probe Annotation GO GUI zebrafish probe
updated 16.3 years ago by 68k • written 16.3 years ago by ▴ 300
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935
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 16.6 years ago by ★ 7.2k • written 16.6 years ago by ▴ 60
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1.8k
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agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
17.0 years ago Georg Otto ▴ 510
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1.0k
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homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
17.6 years ago Mayte Suarez-Farinas ▴ 510
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1.2k
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simpleaffy QCstats and affyQAReport repost
zebrafish probe affy zebrafish probe affy
updated 17.7 years ago by ★ 1.1k • written 17.7 years ago by ▴ 70
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1.4k
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chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ▴ 160
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947
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agilent zebrafish array annotation package
zebrafish zebrafish
19.3 years ago Georg Otto ▴ 510
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1
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1.4k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 19.6 years ago by ▴ 420 • written 19.6 years ago by ▴ 150
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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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1.3k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
19.7 years ago Georg Otto ▴ 510
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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 19.7 years ago by ▴ 780 • written 19.7 years ago by ★ 1.4k
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1.4k
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zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 19.7 years ago by ★ 1.4k • written 19.7 years ago by ★ 1.1k
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4
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1.4k
views
Error in AnnBuilder writeAnnData2Pkg
Annotation zebrafish AnnBuilder Annotation zebrafish AnnBuilder
updated 19.9 years ago by ★ 2.9k • written 19.9 years ago by ▴ 510
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946
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
20.5 years ago Crispin Miller ★ 1.1k
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votes
1
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912
views
problems using cdfenv
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
updated 20.5 years ago by 68k • written 20.5 years ago by ▴ 510
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1
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867
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affymetrix zebrafish chip
zebrafish zebrafish
updated 20.8 years ago by 68k • written 20.8 years ago by ▴ 140
50 results • Page 1 of 1
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Comment: DESeq - help with pair wise comparisons by bd2000 ▴ 30
Follow up question, is this the correct way to extract results? ```r results <- results(ddsObj, list(c("GroupControl.Followup", "GroupTrea…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0
Thank you for your reply! I would love to know your thoughts on the plots I've included above. > 'Are the differences between groups lar…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0
I also realised that the other gene I pointed out that was flagged as DE but had similar count differences also shows that rep1 is lower th…
Comment: DESeq - help with pair wise comparisons by bd2000 ▴ 30
Thanks that's great!! I've followed the instructions from the link you sent, is my code correct? By correct I mean, is my code comparing fo…
Comment: SingleR with multiple single cell references by maltethodberg ▴ 180
Great - the approach with merging the atlases and using `block=` worked well!
Votes
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
Answer: SingleR with multiple single cell references
Answer: SingleR with multiple single cell references
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