Showing : ChIpseq • reset
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123
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 weeks ago yvonneh • 0
0
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1
reply
150
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what is the sampleFiles
chipseq
updated 8 weeks ago by 66k • written 8 weeks ago by • 0
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0
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253
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
4 months ago nilanjanamani88 • 0
1
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3
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464
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 4 months ago by 42k • written 4 months ago by • 0
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0
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213
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
4 months ago frueher • 0
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0
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382
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
7 months ago jared.andrews07 ▴ 30
1
vote
1
reply
513
views
DiffBind - how to prep the sample matrix when multiple bam files are used by MACS2's -t and -c param?
DiffBind chipseq
updated 8 months ago by 66k • written 8 months ago by • 0
0
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0
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321
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
8 months ago franciscrick41 • 0
2
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14
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1.2k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 9 months ago by 66k • written 9 months ago by ▴ 10
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5
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3.6k
views
diffbind
DiffBind chipseq
updated 10 months ago by ★ 5.2k • written 10 months ago by • 0
1
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4
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1.1k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 12 months ago by ★ 5.2k • written 12 months ago by • 0
0
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2
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657
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 13 months ago by ▴ 70 • written 14 months ago by ▴ 140
5
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8
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1.1k
views
Help with error install csaw
ChIPSeq ATACSeq
written 14 months ago by ▴ 10
0
votes
2
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1.2k
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
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0
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472
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
14 months ago Giulia • 0
1
vote
2
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1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
15 months ago chavaleab • 0
1
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3
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734
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
15 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
17 months ago stacy.genovese • 0
0
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2
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823
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
18 months ago stacy.genovese • 0
0
votes
1
reply
910
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 20 months ago by ★ 5.2k • written 20 months ago by • 0
6
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3
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1.4k
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MEDIPS for chIP-Seq
ChIPSeq
written 22 months ago by ▴ 30
0
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7
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1.9k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 22 months ago by ▴ 40 • written 4.2 years ago by ▴ 10
0
votes
1
reply
931
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
23 months ago • updated 22 months ago Jenny Drnevich ★ 2.0k
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0
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725
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intron coordination and annotation
ChIPSeq
updated 23 months ago by ★ 4.2k • written 23 months ago by • 0
0
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0
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857
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Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
24 months ago xubeisi • 0
0
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1
reply
741
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by • 0
0
votes
3
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1.1k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.1 years ago by ★ 5.2k • written 2.1 years ago by • 0
0
votes
0
replies
720
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.1 years ago Swadha • 0
0
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1
reply
898
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.2 years ago by ★ 5.2k • written 2.3 years ago by • 0
1
vote
2
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1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.2 years ago by ★ 5.2k • written 2.2 years ago by • 0
1
vote
1
reply
1.1k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 2.5 years ago by ★ 5.2k • written 2.5 years ago by • 0
0
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0
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772
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.5 years ago Nadav • 0
0
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0
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935
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
2.7 years ago Drew • 0
0
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6
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1.8k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.9 years ago by • 0
3
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12
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3.5k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.8 years ago by ★ 5.2k • written 4.7 years ago by ▴ 20
0
votes
2
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1.2k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.9 years ago • updated 2.8 years ago maria.soler • 0
2
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3
replies
1.5k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.8 years ago by ▴ 20 • written 2.9 years ago by • 0
5
votes
8
replies
2.3k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.0 years ago by ▴ 20 • written 2.9 years ago by ▴ 30
0
votes
1
reply
1.9k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.1 years ago by 66k • written 3.1 years ago by ▴ 290
2
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5
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3.5k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 18 months ago by • 0 • written 3.1 years ago by ★ 5.2k
2
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4
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1.3k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.1 years ago • updated 3.0 years ago richardallenfriedmanbrooklyn ▴ 20
0
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0
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1.7k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.2 years ago Goku • 0
2
votes
6
replies
1.5k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.2 years ago Goku • 0
0
votes
3
replies
1.1k
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 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
1
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4
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1.4k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.3 years ago SFn • 0
0
votes
11
replies
2.1k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
0
votes
2
replies
1.2k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
3.5 years ago indi97 • 0
2
votes
2
replies
2.5k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
3.6 years ago • updated 3.4 years ago Mar Mar ▴ 20
1
vote
4
replies
2.0k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 3.6 years ago by ★ 5.2k • written 6.4 years ago by • 0
2
votes
4
replies
1.8k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 3.6 years ago by ★ 5.2k • written 4.6 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon by silvaesilva.da • 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate by James W. MacDonald 66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Answer: Limma model.matrix design with batch effect and different life stages proportion by Masongeorge • 0
Thanks for this post. i found it helpful for my own issue that was occurring on the backend of this page.
Comment: error loading collectTRI regulon by deeenes ▴ 50
I fixed the original, Ensembl HTTP 403 error only now, [see here][1]. If you've seen it gone earlier today, only shows that this error appe…
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Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
A: Scaling option in fastMNN
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