Showing : ChipSeq • reset
0
votes
1
reply
3.2k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 11.2 years ago by • 0
0
votes
2
replies
600
views
Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 6 months ago by ★ 5.0k • written 7 months ago by • 0
0
votes
0
replies
1.1k
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
8 months ago Muhammad • 0
0
votes
0
replies
394
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
9 months ago atlanta • 0
0
votes
0
replies
382
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
9 months ago info ▴ 10
1
vote
8
replies
2.8k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
10 months ago • updated 9 months ago Luca • 0
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 11 months ago by • 0 • written 11 months ago by • 0
6
votes
5
replies
2.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.5 years ago by ▴ 30
0
votes
0
replies
371
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
14 months ago user_bioinfo • 0
0
votes
0
replies
540
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
16 months ago Alejandro • 0
0
votes
0
replies
851
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
18 months ago gamma.jian ▴ 10
0
votes
0
replies
864
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
20 months ago yvonneh • 0
0
votes
1
reply
619
views
what is the sampleFiles
chipseq
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
0
replies
863
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
23 months ago nilanjanamani88 • 0
1
vote
3
replies
1.2k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 23 months ago by 43k • written 24 months ago by • 0
0
votes
0
replies
639
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
24 months ago frueher • 0
0
votes
0
replies
1.0k
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
2.2 years ago jared.andrews07 ▴ 30
1
vote
1
reply
1.3k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
0
replies
836
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.3 years ago franciscrick41 • 0
2
votes
14
replies
2.7k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
0
votes
5
replies
7.5k
views
diffbind
DiffBind chipseq
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
1
vote
4
replies
2.4k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.6 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
votes
2
replies
1.4k
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.7 years ago by ▴ 70 • written 2.7 years ago by ▴ 140
5
votes
8
replies
1.9k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.8 years ago by ▴ 20
0
votes
2
replies
2.2k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
0
votes
0
replies
853
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.8 years ago Giulia • 0
1
vote
2
replies
1.9k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.9 years ago chavaleab • 0
1
vote
3
replies
1.5k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.9 years ago stacy.genovese • 0
1
vote
4
replies
2.6k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
3.0 years ago stacy.genovese • 0
0
votes
2
replies
1.5k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
3.1 years ago stacy.genovese • 0
0
votes
1
reply
1.4k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.3 years ago by ★ 5.2k • written 3.3 years ago by • 0
0
votes
7
replies
3.0k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.4 years ago by ▴ 40 • written 5.7 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.5 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
intron coordination and annotation
ChIPSeq
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
votes
0
replies
1.4k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.6 years ago xubeisi • 0
0
votes
1
reply
1.2k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
votes
3
replies
1.8k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
0
votes
0
replies
1.2k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.7 years ago Swadha • 0
0
votes
3
replies
1.7k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.9 years ago by • 0
1
vote
2
replies
2.2k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
1
vote
1
reply
1.6k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 4.1 years ago by ★ 5.2k • written 4.1 years ago by • 0
0
votes
0
replies
1.2k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
4.1 years ago Nadav • 0
0
votes
0
replies
1.4k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.3 years ago Drew • 0
0
votes
6
replies
3.1k
views
cel files with affy library
ChIPSeq
updated 4.4 years ago by • 0 • written 4.5 years ago by • 0
3
votes
12
replies
5.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.4 years ago by ★ 5.2k • written 6.3 years ago by ▴ 20
0
votes
2
replies
2.0k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.5 years ago • updated 4.4 years ago maria.soler • 0
2
votes
3
replies
2.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.4 years ago by ▴ 20 • written 4.5 years ago by • 0
5
votes
8
replies
3.4k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.6 years ago by ▴ 20 • written 4.5 years ago by ▴ 30
0
votes
1
reply
2.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 290
2
votes
5
replies
5.8k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.1 years ago by • 0 • written 4.7 years ago by ★ 5.2k
194 results • Page 1 of 4
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Awards • All
Popular Question to nromerov • 0
Popular Question to Thomas Girke ★ 1.7k
Teacher to Gordon Smyth 53k
Popular Question to Stephanie M. Gogarten ▴ 890
Autobiographer to Frances Turner ▴ 20
Locations • All
United States, 20 minutes ago
Iran, 2 hours ago
WEHI, Melbourne, Australia, 2 hours ago
The city by the bay, 2 hours ago
France, 4 hours ago
Traffic: 756 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