Showing : ChipSeq • reset
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Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 10 weeks ago by ★ 4.9k • written 10 weeks ago by • 0
0
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0
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889
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Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
3 months ago Muhammad • 0
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285
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I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
4 months ago atlanta • 0
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0
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260
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
5 months ago • updated 4 months ago info ▴ 10
1
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8
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2.5k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
5 months ago • updated 4 months ago Luca • 0
1
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3
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963
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 7 months ago by • 0 • written 7 months ago by • 0
6
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5
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2.2k
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MEDIPS for chIP-Seq
ChIPSeq
written 3.1 years ago by ▴ 30
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287
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
10 months ago user_bioinfo • 0
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434
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
11 months ago Alejandro • 0
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634
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
14 months ago gamma.jian ▴ 10
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666
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
16 months ago yvonneh • 0
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1
reply
516
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what is the sampleFiles
chipseq
updated 16 months ago by 68k • written 16 months ago by • 0
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742
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
19 months ago nilanjanamani88 • 0
1
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3
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1.0k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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535
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
19 months ago frueher • 0
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0
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886
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
21 months ago jared.andrews07 ▴ 30
1
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1
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1.1k
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 23 months ago by 68k • written 23 months ago by • 0
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0
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672
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
23 months ago franciscrick41 • 0
2
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14
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2.3k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.0 years ago by 68k • written 2.0 years ago by ▴ 10
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5
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diffbind
DiffBind chipseq
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
1
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4
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2.1k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
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2
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1.2k
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.4 years ago by ▴ 70 • written 2.4 years ago by ▴ 140
5
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8
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1.7k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.4 years ago by ▴ 20
0
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2
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2.0k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.4 years ago Giulia • 0
0
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0
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778
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.4 years ago Giulia • 0
1
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2
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1.7k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.5 years ago chavaleab • 0
1
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3
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1.3k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.5 years ago stacy.genovese • 0
1
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4
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2.3k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.7 years ago • updated 2.6 years ago stacy.genovese • 0
0
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2
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1.3k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.8 years ago stacy.genovese • 0
0
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1
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1.3k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
0
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7
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2.7k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.1 years ago by ▴ 40 • written 5.4 years ago by ▴ 10
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1
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1.4k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.1 years ago Jenny Drnevich ★ 2.0k
0
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0
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1.2k
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intron coordination and annotation
ChIPSeq
updated 3.1 years ago by ★ 4.9k • written 3.1 years ago by • 0
0
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0
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1.2k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.2 years ago xubeisi • 0
0
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1
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1.0k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.3 years ago by ★ 1.3k • written 3.3 years ago by • 0
0
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3
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1.6k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
0
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0
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1.0k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.4 years ago Swadha • 0
0
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2
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1.5k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.5 years ago by • 0
1
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2
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2.1k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.5 years ago by ★ 5.2k • written 3.5 years ago by • 0
1
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1
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1.5k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
0
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0
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1.1k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.7 years ago Nadav • 0
0
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0
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1.3k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.9 years ago Drew • 0
0
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6
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2.8k
views
cel files with affy library
ChIPSeq
updated 4.1 years ago by • 0 • written 4.1 years ago by • 0
3
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12
replies
4.9k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.1 years ago by ★ 5.2k • written 6.0 years ago by ▴ 20
0
votes
2
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1.7k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.1 years ago maria.soler • 0
2
votes
3
replies
2.2k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.0 years ago by ▴ 20 • written 4.1 years ago by • 0
5
votes
8
replies
3.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.2 years ago by ▴ 20 • written 4.1 years ago by ▴ 30
0
votes
1
reply
2.5k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 290
2
votes
5
replies
5.4k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.7 years ago by • 0 • written 4.3 years ago by ★ 5.2k
2
votes
4
replies
1.9k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
4.3 years ago richardallenfriedmanbrooklyn ▴ 30
194 results • Page 1 of 4
Recent ...
Replies
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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