Showing : zebrafish • reset
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 7.7 years ago by ★ 4.0k • written 7.7 years ago by ▴ 70
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Importing and Extracting Annotation
annotation zebrafish probe
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
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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
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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
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
9.8 years ago Thomas Maurel ▴ 800
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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
1
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1
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1.8k
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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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1.3k
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ChIPpeakAnno, getAnnotation question
Annotation zebrafish convert biomaRt ChIPpeakAnno Annotation zebrafish convert biomaRt
updated 10.7 years ago by ★ 4.3k • written 10.7 years ago by ▴ 10
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1.4k
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ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 10.7 years ago by ★ 4.3k • written 10.7 years ago by ★ 13k
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1.0k
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affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 10.7 years ago by 65k • written 10.7 years ago by ▴ 80
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2
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1.3k
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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
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0
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1.5k
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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
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1.3k
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Help with Gviz \"IdeogramTrack\" and \"BioMartGeneTrackRegion\" commands
zebrafish biomaRt ideogram genomes zebrafish biomaRt ideogram genomes
11.3 years ago florian.hahne@novartis.com ★ 1.6k
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1.8k
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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
1
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1
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3.0k
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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
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1
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1.4k
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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
12.0 years ago Thomas Maurel ▴ 800
0
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9
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1.9k
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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
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3
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1.7k
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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
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0
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984
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Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
13.6 years ago Neel Aluru ▴ 460
0
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1.1k
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Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
13.6 years ago Neel Aluru ▴ 460
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1
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1.2k
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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
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1
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1.1k
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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
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0
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1.4k
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AgiMicroRna - FilterMicroRna and SignificantMicroRna function
miRNA zebrafish probe AgiMicroRna miRNA zebrafish probe AgiMicroRna
14.0 years ago Neel Aluru ▴ 460
0
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1
reply
963
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
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0
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1.1k
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Ensembl mart release 57: Useful information
SNP GO Homo sapiens zebrafish SNP GO Homo sapiens zebrafish
14.2 years ago Rhoda Kinsella ▴ 660
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6
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1.1k
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annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 14.3 years ago by 65k • written 14.3 years ago by ★ 1.5k
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1
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723
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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 14.3 years ago by ★ 2.0k • written 14.3 years ago by ★ 2.0k
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5
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1.3k
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Agilent zebrafish4x44 database
zebrafish zebrafish
updated 14.5 years ago by ★ 1.3k • written 14.5 years ago by ▴ 460
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0
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814
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Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
14.8 years ago Hervé Pagès 16k
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1
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854
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siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
14.9 years ago Bio Sam ▴ 60
0
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0
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959
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problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
15.0 years ago Georg Otto ▴ 510
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938
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Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
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0
replies
863
views
JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.1 years ago Moshe Pritsker, Editor, JoVE ▴ 20
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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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1.6k
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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 15.4 years ago by 65k • written 15.4 years ago by ▴ 300
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1
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806
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 15.7 years ago by ★ 7.2k • written 15.7 years ago by ▴ 60
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1.5k
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agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.1 years ago Georg Otto ▴ 510
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0
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844
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homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
16.7 years ago Mayte Suarez-Farinas ▴ 510
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2
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998
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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
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3
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1.2k
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chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 17.0 years ago by ★ 7.4k • written 17.0 years ago by ▴ 160
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842
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agilent zebrafish array annotation package
zebrafish zebrafish
18.4 years ago Georg Otto ▴ 510
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1
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1.2k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 18.7 years ago by ▴ 420 • written 18.7 years ago by ▴ 150
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1.2k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.8 years ago Steffen Durinck ▴ 420
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1.1k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.8 years ago Georg Otto ▴ 510
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votes
2
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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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1
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1.3k
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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 18.8 years ago by ★ 1.4k • written 18.8 years ago by ★ 1.1k
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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
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0
replies
830
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
19.6 years ago Crispin Miller ★ 1.1k
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votes
1
reply
769
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
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1
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743
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affymetrix zebrafish chip
zebrafish zebrafish
updated 19.9 years ago by 65k • written 19.9 years ago by ▴ 140
50 results • Page 1 of 1
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Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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