Showing : ChIPseq • reset
0
votes
0
replies
88
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
14 days ago yvonneh • 0
0
votes
1
reply
134
views
what is the sampleFiles
chipseq
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
votes
0
replies
191
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
3 months ago nilanjanamani88 • 0
1
vote
3
replies
426
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
0
replies
188
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
0
votes
0
replies
348
views
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
470
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
votes
0
replies
296
views
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
replies
1.2k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
0
votes
5
replies
3.2k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
vote
4
replies
1.0k
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
2
replies
625
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 13 months ago by ▴ 140
5
votes
8
replies
1.1k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by ▴ 10
0
votes
2
replies
1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago • updated 13 months ago Giulia • 0
0
votes
0
replies
459
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
vote
2
replies
1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
1
vote
3
replies
710
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
15 months ago stacy.genovese • 0
1
vote
4
replies
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
0
votes
2
replies
792
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
0
votes
1
reply
883
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 19 months ago by ★ 5.2k • written 19 months ago by • 0
6
votes
3
replies
1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by ▴ 30
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
votes
0
replies
707
views
intron coordination and annotation
ChIPSeq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
votes
0
replies
820
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
23 months ago xubeisi • 0
0
votes
1
reply
720
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
votes
0
replies
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
879
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
votes
0
replies
750
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
votes
0
replies
914
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 years ago Drew • 0
0
votes
6
replies
1.7k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
3
votes
12
replies
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
votes
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
votes
3
replies
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
5
votes
8
replies
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
votes
1
reply
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
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
2
votes
4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago richardallenfriedmanbrooklyn ▴ 20
0
votes
0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.1 years ago Goku • 0
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
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
vote
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
0
votes
11
replies
2.0k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.3 years ago by • 0 • written 3.3 years ago by • 0
0
votes
2
replies
1.1k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.5 years ago • updated 3.4 years ago indi97 • 0
2
votes
2
replies
2.4k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.5 years ago • updated 3.3 years ago Mar Mar ▴ 20
1
vote
4
replies
2.0k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 3.5 years ago by ★ 5.2k • written 6.3 years ago by • 0
2
votes
4
replies
1.8k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 3.5 years ago by ★ 5.2k • written 4.5 years ago by ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
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
Awards • All
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Michael Love 42k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
The Netherlands, 6 minutes ago
Poland, 14 minutes ago
United States, 22 minutes ago
Greece, 52 minutes ago
Spain, 57 minutes ago
Traffic: 701 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