Showing : ChIPpeakAnno • reset
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How to map geneIds to ENTREZIDs
Xenopus_laevis ChIPpeakAnno
3 days ago stacy.genovese • 0
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153
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Interpretation of $vennCounts output "Others"
ChIPpeakAnno
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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2
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185
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Empty matrix
ChIPpeakAnno Normalization EnrichedHeatmap HELP TxDb.Celegans.UCSC.ce11.refGene
3 months ago michela ▴ 20
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163
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Trying to understand the `select` option in `annotatePeakInBatch` function of `ChIPpeakAnno` package.
ChIPpeakAnno
updated 5 months ago by 62k • written 5 months ago by • 0
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188
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How can I do pathway analysis by ChipPeakAnno package?
ChIPpeakAnno
6 months ago mehdi • 0
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1
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255
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 8 months ago by ★ 1.3k • written 8 months ago by • 0
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1
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326
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peak annotation
ChIPpeakAnno Annotation
updated 9 months ago by ▴ 50 • written 10 months ago by ▴ 660
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720
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another problem when converting bed to granges using togranges
ChIPpeakAnno
11 months ago Bakhtiyar • 0
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2
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397
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ChIP-seq or CUT&RUN enrichment
ChIPQC ChIPpeakAnno
11 months ago Bogdan ▴ 660
2
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6
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924
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Problem converting a bed file to granges using togranges chippeakanno
ChIPpeakAnno
updated 12 months ago by ▴ 50 • written 12 months ago by • 0
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0
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339
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
14 months ago Nadav • 0
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2
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1.1k
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ChIPpeakAnno findOverlapsOfPeaks error: "Error in FUN(X[[i]], ...) : Inputs contains duplicated ranges. please recheck your inputs."
HELP ChIPpeakAnno
14 months ago lexi.kellington • 0
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4
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1.1k
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Error in .order_seqlevels(chrom_sizes[, "chrom"])
ChIPpeakAnno
15 months ago Tongjun • 0
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6
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Annotation by CHIPeakAnno tool
ChIPpeakAnno
19 months ago Arunima ▴ 10
1
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3
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526
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genomicElementDistribution function not found
ChIPpeakAnno
updated 19 months ago by ★ 4.3k • written 19 months ago by ▴ 10
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2
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809
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Hello how to use ChIPpeakAnno for latest version of ensemble genome aligned data
ChIPpeakAnno
23 months ago Lucky • 0
7
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9
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1.1k
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counts of overlapping peaks using findOverlapOfPeaks from ChIPpeakAnno
chippeakanno
updated 2.4 years ago by ★ 4.3k • written 2.4 years ago by ▴ 140
2
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2
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426
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how to suppress makeVennDiagram plot
ChIPpeakAnno
2.5 years ago C T ▴ 140
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2
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514
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How to get 'shortest' distance with ChIPpeakAnno::binOverFeature
ChIPpeakAnno
3.5 years ago liruiradiant • 0
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1
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657
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Unable to annotate in ChIPQC using yeast genome
ChIPQC GenomicRanges ChIPpeakAnno
updated 21 months ago by • 0 • written 3.7 years ago by • 0
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4
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719
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chippeakanno file reading error
ChiPpeakAnno
3.9 years ago saddamhusain77 • 0
1
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6
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781
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how does "maxgap" in ChIPpeakAnno working?
ChIPpeakAnno
4.0 years ago ngs06 ▴ 20
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10
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2.2k
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ChIPpeakAnno, MACS format annotation
bioconductor ChIPpeakAnno
updated 4.1 years ago by ★ 4.3k • written 5.9 years ago by ▴ 30
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7
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
3
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6
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997
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ChIP peak annotation: how to get all genes that overlap each peak?
ChIP-seq chippeakanno chipseeker
4.5 years ago 94133 • 0
0
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1
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741
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Error creating pool for permutation test (PeakPermTest)
permutation pool chippeakanno
4.5 years ago ge2sasag • 0
1
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1
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621
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Row clustering featureAlignedHeatmap function (ChipPeakAnno package)
heatmap chippeakanno
updated 4.8 years ago by ★ 1.3k • written 4.8 years ago by • 0
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2
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1.1k
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Can't install ChIPpeakanno - "libmysqlclient was not found" - do I need to remove latest version of R?
ChIPpeakAnno
updated 5.0 years ago by ★ 5.9k • written 5.0 years ago by ▴ 20
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3
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865
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integer overflow in ChIPpeakAnno assignChromosomeRegion
ChIPpeakAnno assignChromosomeRegion
updated 5.0 years ago by ★ 4.3k • written 5.0 years ago by ▴ 740
1
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1
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592
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Custom regions in assignChromosomeRegion?
chippeakanno
updated 5.0 years ago by ★ 1.3k • written 5.0 years ago by • 0
1
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2
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1.7k
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Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
5.1 years ago inzirio ▴ 10
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4
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1.1k
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ChIPpeakAnno binOverGene error
chippeakanno binOverGene
updated 5.2 years ago by ★ 1.3k • written 5.2 years ago by • 0
0
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1
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821
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ChIPpeakAnno to find peaks nearest to miRNA
ChIPpeakAnno ChIPpeakAnno
updated 5.3 years ago by • 0 • written 10.2 years ago by ▴ 120
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3
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2.1k
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org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 5.3 years ago by • 0 • written 7.3 years ago by • 0
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1
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908
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featureAlignedSignal() error: deparse(sig): object 'sig' not found.
bioconductor chippeakanno featureAlignedDistribution featureAlignedSignal
updated 5.3 years ago by • 0 • written 6.4 years ago by • 0
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693
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Help for ChIP script !! Error message while installing packages
annotation chippeakanno
updated 5.3 years ago by 25k • written 5.3 years ago by • 0
5
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4
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3.3k
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What are out-of-bound ranges? Is it necessary to get rid of them?
r ChIPpeakAnno
5.8 years ago • updated 5.6 years ago salamandra ▴ 20
4
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3
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894
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Annotation Database for ChIPpeakAnno
ChIPpeakAnno
updated 5.6 years ago by ★ 1.3k • written 5.6 years ago by ▴ 110
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785
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Regarding ChIPpeakAnno installation error
chippeakanno
updated 5.8 years ago by 25k • written 5.8 years ago by ▴ 10
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1.7k
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ChIPpeakAnno :findOverlapsOfPeaks: number for overlap peak in venn diagram is different than output of ol1$overlappingPeaks
chippeakanno
updated 5.8 years ago by ★ 1.3k • written 5.8 years ago by • 0
22
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10
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6.8k
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Error in GRanges: could not find symbol "recursive" in environment of the generic function
granges chippeakanno
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 80
2
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3
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1.1k
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ChIPpeakAnno-annotation of peaklist with gene names, creating heat maps
chippeakanno overlappingpeaks annotation
updated 6.1 years ago by ★ 1.3k • written 6.1 years ago by • 0
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7
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2.4k
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ChIPpeakAnno-problem exporting data due to "arguments imply differing number of rows"
chippeakanno
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by • 0
3
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5
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2.5k
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Error with ChIPpeakAnno Ensembl annotation
ChIPpeakAnno genomicfeatures
updated 6.2 years ago by ★ 4.3k • written 6.2 years ago by ▴ 360
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1
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654
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Discordant results in finding overlaps for three peak data with ChIPpeakAnno
ChIPpeakAnno
6.5 years ago moyitasha • 0
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15
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2.3k
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nearest genes using TxDb.Hsapiens.UCSC.hg19
txdb.hsapiens.ucsc.hg19.knowngene ChIPpeakAnno
updated 6.7 years ago by ★ 4.3k • written 6.7 years ago by ▴ 140
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868
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Error with findOverlapsOfPeaks
ChIPpeakAnno
6.8 years ago alex.tamburino • 0
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3
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1.1k
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CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
6.8 years ago lokapal • 0
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2
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1.8k
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Help with toGRanges
granges chippeakanno
updated 6.9 years ago by ★ 1.5k • written 6.9 years ago by • 0
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0
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986
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count overlapping reads for CpG islands and annotate with gene names?
annotation chippeakanno rattus norvegicus medip-seq
6.9 years ago Vang Le ▴ 80
50 results • Page 1 of 1
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Replies
Comment: mas5calls function doesn't work; mirna40cdf problem by Berna • 0
Thank you for the information. I did not know that. Would you have a tip how I could proceed differently?
Comment: Correct use of Likelihood Ratio Test and LFC Shrinkage by ayabalbaa1990 • 0
Hi Michael, So I use this res_LRT <- results(dds_lrt) r2=lfcShrink(dds_lrt, coef=7, res=res_LRT) tu run lfcshrink with LRT, is that oko?…
Comment: Combat and dds Object by shaimaa • 0
I used the combat-seq but the deseq complain as its not integer what should i do
Answer: Different summary() and results() values in DeSeq2 by Basti ▴ 540
summary() tells you the number of genes with low counts, see independant filtering of results in the DESeq2 vignette : https://www.biocondu…
Comment: Atena package - error (new user) by beatriz.calvo ▴ 30
Hi Lalani, We have fixed the bug that lead to the error. The new version of the package (with the bug fixed) will be available in 24-48h. …
Votes
Answer: mas5calls function doesn't work; mirna40cdf problem
Issue with bumphunter and TxDb.Hsapiens.UCSC.hg38.knownGene that could be due to S4Vectors or an installation problem
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
A: How to translate FASTA file of DNA sequence to protein sequence using Biostrings
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