Showing : Chipseq • reset
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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
15 days ago atlanta • 0
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News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
23 days ago • updated 19 days ago info ▴ 10
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 16 days ago Luca • 0
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3
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785
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 12 weeks ago by • 0 • written 3 months ago by • 0
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2.0k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.7 years ago by ▴ 30
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219
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
5 months ago user_bioinfo • 0
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320
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
7 months ago Alejandro • 0
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515
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
10 months ago gamma.jian ▴ 10
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519
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
11 months ago yvonneh • 0
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403
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what is the sampleFiles
chipseq
updated 12 months ago by 68k • written 12 months ago by • 0
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625
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
14 months ago nilanjanamani88 • 0
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3
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881
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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456
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
15 months ago frueher • 0
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769
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
17 months ago jared.andrews07 ▴ 30
1
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970
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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 19 months ago by 68k • written 19 months ago by • 0
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580
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
19 months ago franciscrick41 • 0
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14
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2.0k
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 20 months ago by 68k • written 20 months ago by ▴ 10
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diffbind
DiffBind chipseq
updated 21 months ago by ★ 5.2k • written 21 months ago by • 0
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4
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2.0k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 23 months ago by ★ 5.2k • written 23 months ago by • 0
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1.1k
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.0 years ago by ▴ 70 • written 2.0 years ago by ▴ 140
5
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8
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1.6k
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Help with error install csaw
ChIPSeq ATACSeq
written 2.1 years ago by ▴ 20
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1.8k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.1 years ago Giulia • 0
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687
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.1 years ago Giulia • 0
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1.6k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
2.1 years ago chavaleab • 0
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3
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1.1k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.2 years ago stacy.genovese • 0
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2.0k
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.3 years ago stacy.genovese • 0
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1.2k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.4 years ago stacy.genovese • 0
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1
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1.2k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.6 years ago by • 0
0
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7
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2.5k
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CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.7 years ago by ▴ 40 • written 5.0 years ago by ▴ 10
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1
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1.2k
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Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.8 years ago • updated 2.7 years ago Jenny Drnevich ★ 2.0k
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1.1k
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intron coordination and annotation
ChIPSeq
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.9 years ago xubeisi • 0
0
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1
reply
949
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
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1.5k
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DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
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0
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962
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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
3.0 years ago Swadha • 0
0
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1
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1.2k
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Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
1
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2
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1.9k
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Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
1
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1
reply
1.4k
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DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.3 years ago by ★ 5.2k • written 3.4 years ago by • 0
0
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0
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1.0k
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.4 years ago Nadav • 0
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1.2k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.6 years ago Drew • 0
0
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6
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2.6k
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cel files with affy library
ChIPSeq
updated 3.7 years ago by • 0 • written 3.7 years ago by • 0
3
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12
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4.7k
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.7 years ago by ★ 5.2k • written 5.6 years ago by ▴ 20
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1.6k
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.7 years ago maria.soler • 0
2
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3
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2.0k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.6 years ago by ▴ 20 • written 3.8 years ago by • 0
5
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8
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3.0k
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.9 years ago by ▴ 20 • written 3.8 years ago by ▴ 30
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1
reply
2.4k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.9 years ago by 68k • written 3.9 years ago by ▴ 290
2
votes
5
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5.1k
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.4 years ago by • 0 • written 3.9 years ago by ★ 5.2k
2
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4
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1.7k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
4.0 years ago • updated 3.9 years ago richardallenfriedmanbrooklyn ▴ 30
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2.1k
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4.1 years ago Goku • 0
2
votes
6
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2.0k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4.1 years ago Goku • 0
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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