Showing : Chipseq • reset
0
votes
1
reply
3.0k
views
Job: Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer computational biology rnaseq chipseq Job
written 10.9 years ago by • 0
0
votes
2
replies
484
views
Problem in Chip-seq data analysis using MACS3
chipseq MACSdata
updated 3 months ago by ★ 5.0k • written 3 months ago by • 0
0
votes
0
replies
973
views
Diffbind Analysis gives error during profile plotting stage. Error in value[[3L]](cond) : profileplyr error: Error: BiocParallel errors 1 remote…
chipseq profileplyr DiffBind
5 months ago Muhammad • 0
0
votes
0
replies
314
views
I want my overlapping peaks to stop merging by default doing read counting (using DiffBind in R-studio)
peakoverlap mergingpeaks ChIPseq DiffBind
6 months ago atlanta • 0
0
votes
0
replies
300
views
News: Introduction to Epigenomics data analysis with R and Bioconductor course (online) - 14th-18th April
chipseq MNaseSeq ATACSeq
6 months ago info ▴ 10
1
vote
8
replies
2.6k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
7 months ago • updated 6 months ago Luca • 0
1
vote
3
replies
1.0k
views
Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 8 months ago by • 0 • written 8 months ago by • 0
6
votes
5
replies
2.2k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.2 years ago by ▴ 30
0
votes
0
replies
307
views
ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
11 months ago user_bioinfo • 0
0
votes
0
replies
458
views
Trying to understand basic DiffBind usage
ChIPSeq DiffBind
13 months ago Alejandro • 0
0
votes
0
replies
667
views
Blacklist regions on DBA object (diffbind)
DiffBind chipseq
15 months ago gamma.jian ▴ 10
0
votes
0
replies
719
views
DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
17 months ago yvonneh • 0
0
votes
1
reply
552
views
what is the sampleFiles
chipseq
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
0
replies
767
views
Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
20 months ago nilanjanamani88 • 0
1
vote
3
replies
1.1k
views
Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
0
replies
559
views
Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
21 months ago frueher • 0
0
votes
0
replies
930
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
23 months 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 2.0 years ago by 68k • written 2.0 years ago by • 0
0
votes
0
replies
702
views
Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
2.0 years ago franciscrick41 • 0
2
votes
14
replies
2.4k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
0
votes
5
replies
7.4k
views
diffbind
DiffBind chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
1
vote
4
replies
2.2k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
votes
2
replies
1.3k
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 2.5 years ago by ▴ 70 • written 2.5 years ago by ▴ 140
5
votes
8
replies
1.8k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.5 years ago by ▴ 20
0
votes
2
replies
2.0k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
0
votes
0
replies
800
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
2.6 years ago Giulia • 0
1
vote
2
replies
1.7k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
2.6 years ago chavaleab • 0
1
vote
3
replies
1.3k
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
2.6 years ago stacy.genovese • 0
1
vote
4
replies
2.3k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.8 years ago • updated 2.7 years ago stacy.genovese • 0
0
votes
2
replies
1.4k
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.9 years ago stacy.genovese • 0
0
votes
1
reply
1.3k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.0 years ago by • 0
0
votes
7
replies
2.8k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 3.2 years ago by ▴ 40 • written 5.5 years ago by ▴ 10
0
votes
1
reply
1.4k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.2 years ago Jenny Drnevich ★ 2.0k
0
votes
0
replies
1.2k
views
intron coordination and annotation
ChIPSeq
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
votes
0
replies
1.3k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
3.3 years ago xubeisi • 0
0
votes
1
reply
1.1k
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 3.4 years ago by ★ 1.3k • written 3.4 years ago by • 0
0
votes
3
replies
1.6k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 3.4 years ago by ★ 5.2k • written 3.4 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
3.5 years ago Swadha • 0
0
votes
2
replies
1.6k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
written 3.6 years ago by • 0
1
vote
2
replies
2.1k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
1
vote
1
reply
1.6k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.8 years ago by ★ 5.2k • written 3.8 years ago by • 0
0
votes
0
replies
1.1k
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.8 years ago Nadav • 0
0
votes
0
replies
1.3k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
4.0 years ago Drew • 0
0
votes
6
replies
2.9k
views
cel files with affy library
ChIPSeq
updated 4.2 years ago by • 0 • written 4.2 years ago by • 0
3
votes
12
replies
5.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.2 years ago by ★ 5.2k • written 6.1 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
4.2 years ago maria.soler • 0
2
votes
3
replies
2.3k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 4.1 years ago by ▴ 20 • written 4.2 years ago by • 0
5
votes
8
replies
3.2k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.3 years ago by ▴ 20 • written 4.2 years ago by ▴ 30
0
votes
1
reply
2.6k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 290
2
votes
5
replies
5.5k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.8 years ago by • 0 • written 4.4 years ago by ★ 5.2k
194 results • Page 1 of 4
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Michael Love 43k
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Locations • All
The city by the bay, 1 hour ago
United States, 3 hours ago
Pittsburgh, United States, 5 hours ago
United States, 5 hours ago
United States, 8 hours ago
Traffic: 1253 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