Showing : chipseq • reset
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89
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
15 days ago yvonneh • 0
0
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1
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135
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what is the sampleFiles
chipseq
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
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0
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191
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
3 months ago nilanjanamani88 • 0
1
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3
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427
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
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0
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188
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
1
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3
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1.9k
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
0
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0
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348
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
1
vote
1
reply
471
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 7 months ago by 65k • written 7 months ago by • 0
0
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0
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296
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
7 months ago franciscrick41 • 0
2
votes
14
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1.2k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
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5
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3.2k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
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4
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1.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 11 months ago by ★ 5.2k • written 11 months ago by • 0
0
votes
1
reply
1.2k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 12 months ago by • 0 • written 4.7 years ago by • 0
0
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2
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627
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 13 months ago by ▴ 140
5
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8
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1.1k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by ▴ 10
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2
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1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
0
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0
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459
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
1
vote
2
replies
1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
2
votes
4
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3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 14 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
1
vote
3
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710
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
15 months ago stacy.genovese • 0
1
vote
4
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1.2k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
16 months ago stacy.genovese • 0
2
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5
replies
3.4k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 17 months ago by • 0 • written 3.0 years ago by ★ 5.2k
1
vote
9
replies
3.1k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 17 months ago by ▴ 670 • written 3.6 years ago by ▴ 10
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2
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792
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
6
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3
replies
1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by ▴ 30
0
votes
1
reply
885
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 19 months ago by ★ 5.2k • written 19 months ago by • 0
0
votes
7
replies
1.9k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 21 months ago by ▴ 40 • written 4.1 years ago by ▴ 10
0
votes
1
reply
914
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago • updated 21 months ago Jenny Drnevich ★ 2.0k
0
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0
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708
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intron coordination and annotation
ChIPSeq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
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0
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821
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
23 months ago xubeisi • 0
5
votes
8
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2.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 23 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
0
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1
reply
721
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.0 years ago by ★ 1.3k • written 2.0 years ago by • 0
0
votes
3
replies
1.0k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.0 years ago by ★ 5.2k • written 2.0 years ago by • 0
0
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0
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702
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.1 years ago Swadha • 0
0
votes
1
reply
880
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.2 years ago by • 0
1
vote
2
replies
1.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
1
vote
1
reply
1.0k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
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0
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752
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
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0
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914
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 years ago Drew • 0
2
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3
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1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.7 years ago by ▴ 20 • written 2.8 years ago by • 0
0
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6
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1.7k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
3
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12
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3.4k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.8 years ago by ★ 5.2k • written 4.7 years ago by ▴ 20
0
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2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.8 years ago maria.soler • 0
2
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4
replies
1.3k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago richardallenfriedmanbrooklyn ▴ 20
0
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1
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1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.0 years ago by 65k • written 3.0 years ago by ▴ 290
2
votes
3
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2.4k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.0 years ago by ★ 5.2k • written 6.1 years ago by ▴ 10
2
votes
6
replies
1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.2 years ago • updated 3.1 years ago Goku • 0
0
votes
0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
votes
3
replies
1.0k
views
Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
Deprecation chipseq htseqtools Bioconductor
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
1
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4
replies
1.4k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.3 years ago • updated 3.2 years ago SFn • 0
50 results • Page 1 of 1
Recent ...
Replies
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$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
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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