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 8.1 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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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
9.7 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
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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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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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0
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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 11.7 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
11.9 years ago Thomas Maurel ▴ 800
0
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9
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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
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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
0
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0
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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
0
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0
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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
reply
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
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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
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
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
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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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718
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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 14.3 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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0
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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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834
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siggenes: sam2html + affymetrix zebrafish
zebrafish zebrafish
14.9 years ago Bio Sam ▴ 60
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0
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948
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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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927
views
Ensembl mart release 54: Useful information
Coverage zebrafish Coverage zebrafish
15.0 years ago Rhoda Kinsella ▴ 660
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0
replies
854
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
reply
796
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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832
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
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
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3
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1.1k
views
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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0
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834
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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0
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1.2k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Steffen Durinck ▴ 420
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votes
0
replies
1.1k
views
biomaRt zebrafish
zebrafish biomaRt zebrafish biomaRt
18.7 years ago Georg Otto ▴ 510
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votes
2
replies
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
reply
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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votes
0
replies
823
views
QC questions
zebrafish cdf makecdfenv simpleaffy zebrafish cdf makecdfenv simpleaffy
19.6 years ago Crispin Miller ★ 1.1k
0
votes
1
reply
760
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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733
views
affymetrix zebrafish chip
zebrafish zebrafish
updated 19.8 years ago by 65k • written 19.8 years ago by ▴ 140
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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
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