Showing : chipseq • reset
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158
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
28 days ago Alejandro • 0
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0
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282
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
3 months ago gamma.jian ▴ 10
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0
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290
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
5 months ago yvonneh • 0
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1
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260
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what is the sampleFiles
chipseq
updated 6 months ago by 67k • written 6 months ago by • 0
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0
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424
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
8 months ago nilanjanamani88 • 0
1
vote
3
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621
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 8 months ago by 42k • written 8 months ago by • 0
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0
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323
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
9 months ago frueher • 0
0
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0
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577
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
11 months ago jared.andrews07 ▴ 30
1
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1
reply
708
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DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 12 months ago by 67k • written 12 months ago by • 0
0
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0
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445
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
12 months ago franciscrick41 • 0
2
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14
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1.6k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 13 months ago by 67k • written 13 months ago by ▴ 10
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5
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5.8k
views
diffbind
DiffBind chipseq
updated 14 months ago by ★ 5.2k • written 14 months ago by • 0
1
vote
4
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1.5k
views
DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 16 months ago by ★ 5.2k • written 16 months ago by • 0
0
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2
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825
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 17 months ago by ▴ 70 • written 18 months ago by ▴ 140
5
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8
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1.3k
views
Help with error install csaw
ChIPSeq ATACSeq
written 18 months ago by ▴ 20
0
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2
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1.5k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
19 months ago Giulia • 0
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0
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565
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
19 months ago Giulia • 0
1
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2
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1.4k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
19 months ago chavaleab • 0
1
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3
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907
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
20 months ago stacy.genovese • 0
1
vote
4
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1.5k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
21 months ago stacy.genovese • 0
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2
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972
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
22 months ago stacy.genovese • 0
0
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1
reply
1.0k
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.0 years ago by ★ 5.2k • written 2.0 years ago by • 0
6
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3
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1.7k
views
MEDIPS for chIP-Seq
ChIPSeq
written 2.2 years ago by ▴ 30
0
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7
replies
2.2k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.2 years ago by ▴ 40 • written 4.5 years ago by ▴ 10
0
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1
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1.1k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.2 years ago Jenny Drnevich ★ 2.0k
0
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0
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887
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intron coordination and annotation
ChIPSeq
updated 2.2 years ago by ★ 4.5k • written 2.2 years ago by • 0
0
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0
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986
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.3 years ago xubeisi • 0
0
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1
reply
834
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.4 years ago by ★ 1.3k • written 2.4 years ago by • 0
0
votes
3
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1.3k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.4 years ago by ★ 5.2k • written 2.4 years ago by • 0
0
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0
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832
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.5 years ago Swadha • 0
0
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1
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1.0k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.5 years ago by ★ 5.2k • written 2.6 years ago by • 0
1
vote
2
replies
1.5k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.6 years ago by ★ 5.2k • written 2.6 years ago by • 0
1
vote
1
reply
1.2k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.8 years ago by ★ 5.2k • written 2.8 years ago by • 0
0
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0
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913
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.9 years ago Nadav • 0
0
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0
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1.1k
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.0 years ago Drew • 0
0
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6
replies
2.1k
views
cel files with affy library
ChIPSeq
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
3
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12
replies
4.0k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.2 years ago by ★ 5.2k • written 5.1 years ago by ▴ 20
0
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2
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1.3k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.2 years ago maria.soler • 0
2
votes
3
replies
1.8k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.1 years ago by ▴ 20 • written 3.2 years ago by • 0
5
votes
8
replies
2.5k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.4 years ago by ▴ 20 • written 3.2 years ago by ▴ 30
0
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1
reply
2.1k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.4 years ago by 67k • written 3.4 years ago by ▴ 290
2
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5
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4.1k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 22 months ago by • 0 • written 3.4 years ago by ★ 5.2k
2
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4
replies
1.5k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.4 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
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1.9k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.6 years ago Goku • 0
2
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6
replies
1.7k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.6 years ago Goku • 0
0
votes
3
replies
1.2k
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 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
1
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4
replies
1.6k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.7 years ago • updated 3.6 years ago SFn • 0
0
votes
11
replies
2.3k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.7 years ago by • 0 • written 3.8 years ago by • 0
0
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2
replies
1.3k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.9 years ago indi97 • 0
2
votes
2
replies
2.7k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.9 years ago • updated 3.7 years ago Mar Mar ▴ 20
50 results • Page 1 of 1
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Replies
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Comment: When running contrasts, does it use normalized read counts? by Katherine • 0
Ok, so the comment I was given where they said DeSeq2 should be with normalized counts is incorrect. the ```normalized_counts``` variable …
Answer: How to reverse complement some elements of a DNAStringSet by James W. MacDonald 67k
You should always try the vectorized method first, rather than looping. ``` > myFasta[myFasta_rc] <- reverseComplement(myFasta[myFasta_…
Answer: When running contrasts, does it use normalized read counts? by James W. MacDonald 67k
A contrast is a comparison of two or more coefficients. When you run `nbiomWaldTest` you are fitting the GLM and estimating coefficients. T…
Comment: Too much data for Diffbind by Ou, Jianhong ★ 1.3k
Just in case if somebody still want to apply summits greater than 0 and got the same error, you can filter out the peaks with start positio…
Votes
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
What should be the normalization protocol for RNA seq data for WGCNA?
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Scholar to James W. MacDonald 67k
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