Showing : ChipSeq • reset
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
20 minutes ago user_bioinfo • 0
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182
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
7 weeks ago Alejandro • 0
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316
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
4 months ago gamma.jian ▴ 10
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317
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 months ago yvonneh • 0
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1
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286
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what is the sampleFiles
chipseq
updated 6 months ago by 67k • written 6 months ago by • 0
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440
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
9 months ago nilanjanamani88 • 0
1
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3
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646
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 9 months ago by 42k • written 9 months ago by • 0
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342
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
9 months ago frueher • 0
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602
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
11 months ago jared.andrews07 ▴ 30
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1
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732
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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 13 months ago by 67k • written 13 months ago by • 0
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460
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
13 months ago franciscrick41 • 0
2
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14
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1.6k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 14 months ago by 67k • written 14 months ago by ▴ 10
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5
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6.3k
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diffbind
DiffBind chipseq
updated 15 months ago by ★ 5.2k • written 15 months ago by • 0
1
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4
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1.6k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 17 months ago by ★ 5.2k • written 17 months ago by • 0
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2
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848
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 18 months ago by ▴ 70 • written 18 months ago by ▴ 140
5
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8
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1.4k
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Help with error install csaw
ChIPSeq ATACSeq
written 19 months ago by ▴ 20
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2
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1.5k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
19 months ago Giulia • 0
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0
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585
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
19 months ago Giulia • 0
1
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2
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1.4k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
20 months ago chavaleab • 0
1
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3
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925
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
20 months ago stacy.genovese • 0
1
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1.6k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
22 months ago • updated 21 months ago stacy.genovese • 0
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2
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991
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
23 months ago stacy.genovese • 0
0
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1
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1.1k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
6
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3
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1.7k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.3 years ago by ▴ 30
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7
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2.2k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.2 years ago by ▴ 40 • written 4.5 years ago by ▴ 10
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1
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1.1k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.3 years ago Jenny Drnevich ★ 2.0k
0
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913
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intron coordination and annotation
ChIPSeq
updated 2.3 years ago by ★ 4.5k • written 2.3 years ago by • 0
0
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0
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997
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.4 years ago xubeisi • 0
0
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1
reply
850
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AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
0
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3
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1.3k
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
0
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0
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845
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.5 years ago Swadha • 0
0
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1
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1.1k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
1
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2
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1.6k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
1
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1
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1.3k
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
0
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0
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928
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.9 years ago Nadav • 0
0
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0
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1.1k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.1 years ago Drew • 0
0
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6
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2.2k
views
cel files with affy library
ChIPSeq
updated 3.2 years ago by • 0 • written 3.3 years ago by • 0
3
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12
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4.1k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.2 years ago by ★ 5.2k • written 5.1 years ago by ▴ 20
0
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2
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1.4k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.3 years ago • updated 3.2 years ago maria.soler • 0
2
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3
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1.8k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.2 years ago by ▴ 20 • written 3.3 years ago by • 0
5
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8
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2.6k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.4 years ago by ▴ 20 • written 3.3 years ago by ▴ 30
0
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1
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2.1k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.4 years ago by 67k • written 3.4 years ago by ▴ 290
2
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5
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4.2k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 23 months ago by • 0 • written 3.5 years ago by ★ 5.2k
2
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4
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1.5k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.5 years ago • updated 3.4 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
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1.9k
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.6 years ago Goku • 0
2
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6
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1.7k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.6 years ago Goku • 0
0
votes
3
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1.2k
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 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
1
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4
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1.6k
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.7 years ago SFn • 0
0
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11
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2.3k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.8 years ago by • 0 • written 3.8 years ago by • 0
0
votes
2
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1.4k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.9 years ago indi97 • 0
50 results • Page 1 of 1
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Replies
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Adam Marstrand • 0
Hi again, Thank you for the response! Can you expound on why it is not a good idea? I realize that the expression levels/differential expr…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by James W. MacDonald 67k
No, that's not a good idea at all. You should be doing a meta-analysis with these data rather than trying to combine like that. `GeneMeta` …
Answer: GOstats kegg analysis in wheat - help - none of the objects in the first column by James W. MacDonald 67k
Check the help page for `KEGGFrame`. Your columns are out of order.
Comment: Question about using LRT test for time course experiments with DESeq2 by James W. MacDonald 67k
You are testing the interaction, so you are asking for those genes that change at any time *differently, depending on the treatment*. If co…
Comment: DESeq Input from Salmon + tximport/tximeta by LuciaNhu • 0
Thank you both. Special thanks from Prof. Michael Love. It's rare to find tool authors who respond to users so quickly and supportively. Ma…
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Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
Answer: DESeq Input from Salmon + tximport/tximeta
Answer: featureCounts segmentation fault with large chromosomes
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