Showing : zebrafish • reset
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2.2k
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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
1
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1
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1.8k
views
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
1
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1
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2.9k
views
goseq/nullp with non-native identifiers
Annotation GO zebrafish goseq Annotation GO zebrafish goseq
updated 11.6 years ago by ▴ 100 • written 11.7 years ago by ▴ 140
0
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1
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733
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affymetrix zebrafish chip
zebrafish zebrafish
updated 19.8 years ago by 65k • written 19.8 years ago by ▴ 140
0
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1
reply
760
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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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0
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823
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QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
19.6 years ago Crispin Miller ★ 1.1k
0
votes
4
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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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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
0
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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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0
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1.1k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Georg Otto ▴ 510
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0
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1.2k
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biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Steffen Durinck ▴ 420
0
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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
0
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0
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834
views
agilent zebrafish array annotation package
zebrafish zebrafish
18.3 years ago Georg Otto ▴ 510
0
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3
replies
1.1k
views
chromosome plot
zebrafish geneplotter zebrafish geneplotter
updated 16.9 years ago by ★ 7.4k • written 16.9 years ago by ▴ 160
0
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2
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988
views
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
0
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0
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832
views
homologs for xenopus laevis
Xenopus laevis zebrafish biomaRt Xenopus laevis zebrafish biomaRt
16.6 years ago Mayte Suarez-Farinas ▴ 510
0
votes
2
replies
1.5k
views
agilent zebrafish array annotation
Annotation zebrafish AnnBuilder PROcess AnnotationDbi Annotation zebrafish AnnBuilder
16.0 years ago Georg Otto ▴ 510
0
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1
reply
796
views
zebrafish annotation
Annotation zebrafish Annotation zebrafish
updated 15.6 years ago by ★ 7.2k • written 15.6 years ago by ▴ 60
0
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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
0
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1
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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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0
replies
852
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JoVE: New Video Articles on Biomedical Research Techniques
zebrafish zebrafish
15.0 years ago Moshe Pritsker, Editor, JoVE ▴ 20
0
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0
replies
927
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
947
views
problem using annotation database with annaffy
Annotation GO zebrafish annaffy Annotation GO zebrafish annaffy
14.9 years ago Georg Otto ▴ 510
0
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1
reply
834
views
siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
14.9 years ago Bio Sam ▴ 60
0
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0
replies
807
views
Bsgenome Zv7 sequence data
Cancer Danio rerio zebrafish Cancer Danio rerio zebrafish
14.7 years ago Hervé Pagès 16k
0
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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
0
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1
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718
views
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
0
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6
replies
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
0
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0
replies
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
0
votes
1
reply
948
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
0
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0
replies
1.4k
views
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
1.1k
views
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
0
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1
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1.1k
views
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
0
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0
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977
views
Agi4x44PreProcess - filter.probes function
Annotation GUI zebrafish probe PROcess Annotation GUI zebrafish probe PROcess
13.5 years ago Neel Aluru ▴ 460
0
votes
3
replies
1.6k
views
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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9
replies
1.9k
views
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
0
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1
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1.4k
views
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
votes
2
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1.8k
views
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
0
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0
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1.3k
views
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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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
0
votes
2
replies
1.3k
views
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
0
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1
reply
1.0k
views
affymtrix transcript_cluster categories
Normalization zebrafish Normalization zebrafish
updated 10.6 years ago by 65k • written 10.6 years ago by ▴ 80
0
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1
reply
1.3k
views
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
0
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1
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1.3k
views
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
0
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2
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1.8k
views
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
0
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0
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1.3k
views
Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
9.7 years ago Thomas Maurel ▴ 800
0
votes
2
replies
1.1k
views
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
0
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1
reply
1.3k
views
Importing and Extracting Annotation
annotation zebrafish probe
updated 8.0 years ago by 65k • written 8.1 years ago by • 0
0
votes
0
replies
1.1k
views
Agi4x44PreProcess
GUI zebrafish probe AgiMicroRna GUI zebrafish probe AgiMicroRna
13.6 years ago Neel Aluru ▴ 460
0
votes
2
replies
1.4k
views
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
50 results • Page 1 of 1
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Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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