Showing : Chipseq • reset
0
votes
1
reply
69
views
what is the sampleFiles
chipseq
updated 2 days ago by 65k • written 2 days ago by • 0
0
votes
0
replies
138
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
10 weeks ago nilanjanamani88 • 0
1
vote
3
replies
363
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 11 weeks ago by 41k • written 12 weeks ago by • 0
0
votes
0
replies
159
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
1
vote
3
replies
1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.1k • written 6.5 years ago by • 0
0
votes
0
replies
312
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
1
vote
1
reply
423
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 6 months ago by 65k • written 6 months ago by • 0
0
votes
0
replies
269
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
6 months ago franciscrick41 • 0
2
votes
14
replies
1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 7 months ago by 65k • written 8 months ago by ▴ 10
0
votes
5
replies
2.9k
views
diffbind
DiffBind chipseq
updated 8 months ago by ★ 5.1k • written 8 months ago by • 0
1
vote
4
replies
986
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 10 months ago by ★ 5.1k • written 11 months ago by • 0
0
votes
1
reply
1.1k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 11 months ago by • 0 • written 4.6 years ago by • 0
0
votes
2
replies
588
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 11 months ago by ▴ 70 • written 12 months ago by ▴ 140
5
votes
8
replies
991
views
Help with error install csaw
ChIPSeq ATACSeq
written 12 months ago by • 0
0
votes
2
replies
1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
0
votes
0
replies
437
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
13 months ago chavaleab • 0
2
votes
4
replies
3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 13 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
1
vote
3
replies
671
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
14 months ago stacy.genovese • 0
1
vote
4
replies
1.1k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
15 months ago stacy.genovese • 0
2
votes
5
replies
3.3k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 16 months ago by • 0 • written 2.9 years ago by ★ 5.1k
1
vote
9
replies
2.9k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 16 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
0
votes
2
replies
750
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago • updated 16 months ago stacy.genovese • 0
6
votes
3
replies
1.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 20 months ago by ▴ 30
0
votes
1
reply
854
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 18 months ago by ★ 5.1k • written 18 months ago by • 0
0
votes
7
replies
1.8k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 20 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
0
votes
1
reply
889
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago • updated 20 months ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
680
views
intron coordination and annotation
ChIPSeq
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
votes
0
replies
773
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
22 months ago xubeisi • 0
5
votes
8
replies
2.1k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 22 months ago by ▴ 20 • written 2.8 years ago by ▴ 30
0
votes
1
reply
692
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
votes
3
replies
993
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 23 months ago by ★ 5.1k • written 23 months ago by • 0
0
votes
0
replies
677
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
24 months ago Swadha • 0
0
votes
1
reply
843
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.0 years ago by ★ 5.1k • written 2.1 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 2.1 years ago by ★ 5.1k • written 2.1 years ago by • 0
1
vote
1
reply
997
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.3 years ago by ★ 5.1k • written 2.3 years ago by • 0
0
votes
0
replies
725
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
votes
0
replies
888
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.5 years ago Drew • 0
2
votes
3
replies
1.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.6 years ago by ▴ 20 • written 2.7 years ago by • 0
0
votes
6
replies
1.6k
views
cel files with affy library
ChIPSeq
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
3
votes
12
replies
3.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.7 years ago by ★ 5.1k • written 4.6 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.7 years ago maria.soler • 0
2
votes
4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
2.9 years ago richardallenfriedmanbrooklyn ▴ 20
0
votes
1
reply
1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.9 years ago by 65k • written 2.9 years ago by ▴ 270
2
votes
3
replies
2.3k
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 ★ 5.1k • written 6.0 years ago by ▴ 10
2
votes
6
replies
1.4k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
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 3.1 years ago by ▴ 770 • written 3.1 years ago by • 0
1
vote
4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.2 years ago • updated 3.1 years ago SFn • 0
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.2 years ago by • 0 • written 3.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Awards • All
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Popular Question to W. Evan Johnson ▴ 850
Popular Question to Alejandro Reyes ★ 1.9k
Locations • All
WEHI, Melbourne, Australia, just now
China, just now
The city by the bay, 2 minutes ago
Mexico, 15 minutes ago
Thailand, 19 minutes ago
Traffic: 554 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6