Showing : zebrafish • reset
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Need help annotating Affymetrix 1.1ST microarrays
oligo annotation affymetrix microarrays zebrafish
updated 7.6 years ago by ★ 3.9k • written 7.6 years ago by ▴ 70
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Importing and Extracting Annotation
annotation zebrafish probe
updated 8.0 years ago by 65k • written 8.0 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 8.9 years ago by ▴ 390 • written 8.9 years ago by ▴ 800
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1.1k
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Interspecies differential expression of orthologs with Edger
RNASeq Normalization Organism zebrafish edgeR
updated 9.6 years ago by 50k • written 9.6 years ago by ▴ 140
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
9.7 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
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1.3k
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ChIPpeakAnno, getAnnotation question
Annotation zebrafish convert biomaRt ChIPpeakAnno Annotation zebrafish convert biomaRt
updated 10.6 years ago by ★ 4.3k • written 10.6 years ago by ▴ 10
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1.3k
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ChIPpeakAnno, getAnnotation question
Annotation GO zebrafish convert biomaRt ChIPpeakAnno Annotation GO zebrafish convert
updated 10.6 years ago by ★ 4.3k • written 10.6 years ago by ★ 13k
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1.0k
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affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 10.6 years ago by 65k • written 10.6 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 10.6 years ago by 65k • written 10.6 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
11.0 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
11.2 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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2.9k
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goseq/nullp with non-native identifiers
Annotation GO zebrafish goseq Annotation GO zebrafish goseq
updated 11.6 years ago by ▴ 100 • written 11.6 years ago by ▴ 140
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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
11.9 years ago Thomas Maurel ▴ 800
0
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9
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1.8k
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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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1.6k
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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
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977
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Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
13.5 years ago Neel Aluru ▴ 460
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1.1k
views
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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1.1k
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Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 13.7 years ago by ★ 7.2k • written 13.7 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
13.9 years ago Neel Aluru ▴ 460
0
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1
reply
946
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
views
Ensembl mart release 57: Useful information
SNP GO Homo sapiens zebrafish SNP GO Homo sapiens zebrafish
14.1 years ago Rhoda Kinsella ▴ 660
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6
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1.1k
views
annaffy can't saveHTML
Annotation zebrafish Annotation zebrafish
updated 14.2 years ago by 65k • written 14.2 years ago by ★ 1.5k
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1
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715
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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 14.2 years ago by ★ 2.0k • written 14.2 years ago by ★ 2.0k
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5
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1.3k
views
Agilent zebrafish4x44 database
zebrafish zebrafish
updated 14.5 years ago by ★ 1.3k • written 14.5 years ago by ▴ 460
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807
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Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
14.7 years ago Hervé Pagès 16k
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1
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832
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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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945
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problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
14.9 years ago Georg Otto ▴ 510
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0
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926
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
0
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0
replies
852
views
JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.0 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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2
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1.6k
views
Help with loading newly created custom annotation db into R session
Annotation GO GUI zebrafish probe Annotation GO GUI zebrafish probe
updated 15.3 years ago by 65k • written 15.3 years ago by ▴ 300
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1
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795
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 15.6 years ago by ★ 7.2k • written 15.6 years ago by ▴ 60
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2
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1.5k
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agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.0 years ago Georg Otto ▴ 510
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0
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829
views
homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
16.6 years ago Mayte Suarez-Farinas ▴ 510
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2
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988
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simpleaffy QCstats and affyQAReport repost
zebrafish probe affy zebrafish probe affy
updated 16.7 years ago by ★ 1.1k • written 16.7 years ago by ▴ 70
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3
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1.1k
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chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 160
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832
views
agilent zebrafish array annotation package
zebrafish zebrafish
18.3 years ago Georg Otto ▴ 510
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1
reply
1.2k
views
biomaRt gives only NA output
drosgenome1 zebrafish biomaRt drosgenome1 zebrafish biomaRt
updated 18.6 years ago by ▴ 420 • written 18.6 years ago by ▴ 150
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1.2k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Steffen Durinck ▴ 420
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0
replies
1.1k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Georg Otto ▴ 510
0
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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1.2k
views
zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds
zebrafish cdf probe reposTools gcrma matchprobes simpleaffy zebrafish cdf probe gcrma
updated 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
822
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
19.5 years ago Crispin Miller ★ 1.1k
0
votes
1
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760
views
problems using cdfenv
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
updated 19.5 years ago by 65k • written 19.5 years ago by ▴ 510
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1
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732
views
affymetrix zebrafish chip
zebrafish zebrafish
updated 19.8 years ago by 65k • written 19.8 years ago by ▴ 140
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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