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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Importing and Extracting Annotation
annotation zebrafish probe
updated 8.9 years ago by 68k • written 9.0 years ago by • 0
9
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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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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
10.6 years ago Thomas Maurel ▴ 800
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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 11.5 years ago by ▴ 10
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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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1.2k
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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 11.6 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
12.1 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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3.3k
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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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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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2.2k
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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
14.4 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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1.3k
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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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1.3k
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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
14.8 years ago Neel Aluru ▴ 460
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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
15.0 years ago Rhoda Kinsella ▴ 660
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1.3k
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annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 15.1 years ago by 68k • written 15.1 years ago by ★ 1.5k
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848
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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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935
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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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984
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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
15.8 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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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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931
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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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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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
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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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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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943
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agilent zebrafish array annotation package
zebrafish zebrafish
19.2 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 19.5 years ago by ▴ 420 • written 19.5 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
19.6 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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1.3k
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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943
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QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
20.5 years ago Crispin Miller ★ 1.1k
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1
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908
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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860
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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 ...
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Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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