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 11.1 years ago by • 0
0
votes
2
replies
555
views
Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 5 months ago by ★ 5.0k • written 5 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
6 months ago Muhammad • 0
0
votes
0
replies
350
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
7 months ago atlanta • 0
0
votes
0
replies
341
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
8 months ago • updated 7 months ago info ▴ 10
1
vote
8
replies
2.7k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
8 months ago • updated 7 months ago Luca • 0
1
vote
3
replies
1.2k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 10 months ago by • 0 • written 10 months ago by • 0
6
votes
5
replies
2.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.3 years ago by ▴ 30
0
votes
0
replies
330
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
13 months ago user_bioinfo • 0
0
votes
0
replies
508
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
14 months ago Alejandro • 0
0
votes
0
replies
806
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
17 months ago gamma.jian ▴ 10
0
votes
0
replies
811
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
19 months ago yvonneh • 0
0
votes
1
reply
595
views
what is the sampleFiles
chipseq
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
0
replies
805
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
22 months ago nilanjanamani88 • 0
1
vote
3
replies
1.1k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
0
replies
601
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
22 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
2.0 years ago jared.andrews07 ▴ 30
1
vote
1
reply
1.2k
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
0
replies
797
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.2 years ago franciscrick41 • 0
2
votes
14
replies
2.5k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
0
votes
5
replies
7.4k
views
diffbind
DiffBind chipseq
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
1
vote
4
replies
2.3k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
0
votes
2
replies
1.3k
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.6 years ago by ▴ 70 • written 2.6 years ago by ▴ 140
5
votes
8
replies
1.9k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.7 years ago by ▴ 20
0
votes
2
replies
2.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
0
votes
0
replies
832
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.7 years ago Giulia • 0
1
vote
2
replies
1.8k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.7 years ago chavaleab • 0
1
vote
3
replies
1.4k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.8 years ago stacy.genovese • 0
1
vote
4
replies
2.4k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.9 years ago stacy.genovese • 0
0
votes
2
replies
1.5k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
3.0 years ago stacy.genovese • 0
0
votes
1
reply
1.4k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.2 years ago by • 0
0
votes
7
replies
2.9k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.3 years ago by ▴ 40 • written 5.6 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
3.4 years ago • updated 3.3 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.3k
views
intron coordination and annotation
ChIPSeq
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.5 years ago xubeisi • 0
0
votes
1
reply
1.1k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.5 years ago by ★ 1.3k • written 3.5 years ago by • 0
0
votes
3
replies
1.7k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
0
votes
0
replies
1.1k
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
3.6 years ago Swadha • 0
0
votes
3
replies
1.6k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.7 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 3.7 years ago by ★ 5.2k • written 3.7 years ago by • 0
1
vote
1
reply
1.6k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.9 years ago by ★ 5.2k • written 4.0 years ago by • 0
0
votes
0
replies
1.2k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
4.0 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
4.2 years ago Drew • 0
0
votes
6
replies
3.0k
views
cel files with affy library
ChIPSeq
updated 4.3 years ago by • 0 • written 4.3 years ago by • 0
3
votes
12
replies
5.1k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.3 years ago by ★ 5.2k • written 6.2 years ago by ▴ 20
0
votes
2
replies
1.8k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.3 years ago maria.soler • 0
2
votes
3
replies
2.4k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.2 years ago by ▴ 20 • written 4.3 years ago by • 0
5
votes
8
replies
3.3k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.5 years ago by ▴ 20 • written 4.4 years ago by ▴ 30
0
votes
1
reply
2.7k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 290
2
votes
5
replies
5.7k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 3.0 years ago by • 0 • written 4.5 years ago by ★ 5.2k
194 results • Page 1 of 4
Recent ...
Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to k___ ▴ 30
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Locations • All
Germany, 18 minutes ago
United States, 50 minutes ago
The city by the bay, 2 hours ago
United States, 2 hours ago
United States, 2 hours ago
Traffic: 909 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