Showing : ChipSeq • reset
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45
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
4 days ago yvonneh • 0
0
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1
reply
120
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what is the sampleFiles
chipseq
updated 20 days ago by 65k • written 20 days ago by • 0
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0
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170
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
12 weeks ago nilanjanamani88 • 0
1
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3
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397
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
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0
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176
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
3 months ago frueher • 0
1
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3
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1.8k
views
DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 4 months ago by ★ 5.2k • written 6.6 years ago by • 0
0
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0
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333
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
5 months ago jared.andrews07 ▴ 30
1
vote
1
reply
453
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
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0
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286
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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
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1.1k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 8 months ago by 65k • written 8 months ago by ▴ 10
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5
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3.1k
views
diffbind
DiffBind chipseq
updated 9 months ago by ★ 5.2k • written 9 months ago by • 0
1
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4
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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
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1
reply
1.2k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 12 months ago by • 0 • written 4.7 years ago by • 0
0
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2
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611
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 12 months ago by ▴ 140
5
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8
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1.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 13 months ago by • 0
0
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2
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1.1k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
0
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0
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450
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
vote
2
replies
1.0k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
2
votes
4
replies
3.4k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 14 months ago by ▴ 10 • written 7.2 years ago by ▴ 40
1
vote
3
replies
696
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
14 months ago stacy.genovese • 0
1
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4
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1.2k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
16 months ago • updated 15 months ago stacy.genovese • 0
2
votes
5
replies
3.3k
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
1
vote
9
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3.0k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 17 months ago by ▴ 670 • written 3.5 years ago by ▴ 10
0
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2
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778
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
17 months ago stacy.genovese • 0
6
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3
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1.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 21 months ago by ▴ 30
0
votes
1
reply
874
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 19 months ago by ★ 5.2k • written 19 months ago by • 0
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 4.0 years ago by ▴ 10
0
votes
1
reply
905
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
21 months ago Jenny Drnevich ★ 2.0k
0
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0
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697
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intron coordination and annotation
ChIPSeq
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
0
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0
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803
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
22 months ago xubeisi • 0
5
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8
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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
711
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 24 months ago by ★ 1.3k • written 24 months ago by • 0
0
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3
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1.0k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 24 months ago by ★ 5.2k • written 24 months ago by • 0
0
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0
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692
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.0 years ago Swadha • 0
0
votes
1
reply
863
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 2.1 years ago by ★ 5.2k • written 2.1 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
743
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.4 years ago Nadav • 0
0
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0
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906
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.6 years ago Drew • 0
2
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3
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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
0
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6
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1.7k
views
cel files with affy library
ChIPSeq
updated 2.7 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 2.7 years ago by ★ 5.2k • written 4.6 years ago by ▴ 20
0
votes
2
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1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.8 years ago • updated 2.7 years ago maria.soler • 0
2
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4
replies
1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 years ago • updated 2.9 years ago richardallenfriedmanbrooklyn ▴ 20
0
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1
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1.8k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.9 years ago by 65k • written 2.9 years ago by ▴ 280
2
votes
3
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2.4k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.0 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
2
votes
6
replies
1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.1 years ago Goku • 0
0
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0
replies
1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
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
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4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.2 years ago SFn • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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