Showing : ChipSeq • reset
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Csaw normalization strategies - general inquiry
ChIPSeq csaw
updated 4 days ago by • 0 • written 7 days ago by • 0
6
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5
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1.9k
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MEDIPS for chIP-Seq
ChIPSeq
written 2.5 years ago by ▴ 30
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0
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167
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ChIP peaks comparison
ChIPSeqData genomes ChIPSeq
12 weeks ago user_bioinfo • 0
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0
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256
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Trying to understand basic DiffBind usage
ChIPSeq DiffBind
4 months ago Alejandro • 0
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0
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423
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Blacklist regions on DBA object (diffbind)
DiffBind chipseq
7 months ago gamma.jian ▴ 10
0
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0
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418
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
9 months ago yvonneh • 0
0
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1
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338
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what is the sampleFiles
chipseq
updated 9 months ago by 67k • written 9 months ago by • 0
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0
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536
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
11 months ago nilanjanamani88 • 0
1
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3
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743
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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0
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403
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
12 months ago frueher • 0
0
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0
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681
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
14 months ago jared.andrews07 ▴ 30
1
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1
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829
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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 16 months ago by 67k • written 16 months ago by • 0
0
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0
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518
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Why there are two pfms in the result of oligoSummary function of ChIPpeakAnno package?
ChIPpeakAnno ChIPSeq MotifDiscovery
16 months ago franciscrick41 • 0
2
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14
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1.8k
views
ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 17 months ago by 67k • written 17 months ago by ▴ 10
0
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5
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6.8k
views
diffbind
DiffBind chipseq
updated 18 months ago by ★ 5.2k • written 18 months ago by • 0
1
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4
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1.8k
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 20 months ago by ★ 5.2k • written 20 months ago by • 0
0
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2
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948
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 140
5
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8
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1.5k
views
Help with error install csaw
ChIPSeq ATACSeq
written 22 months ago by ▴ 20
0
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2
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1.7k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
0
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0
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637
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
22 months ago Giulia • 0
1
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2
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1.5k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
23 months ago chavaleab • 0
1
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3
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1.0k
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Only getting 10 peaks from mac2 callpeak
ChIPSeq
23 months ago stacy.genovese • 0
1
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4
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1.7k
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
2.1 years ago • updated 2.0 years ago stacy.genovese • 0
0
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2
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1.1k
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New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
2.2 years ago stacy.genovese • 0
0
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1
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1.1k
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 2.3 years ago by ★ 5.2k • written 2.3 years ago by • 0
0
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7
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2.4k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 2.5 years ago by ▴ 40 • written 4.8 years ago by ▴ 10
0
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1
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1.2k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
2.5 years ago Jenny Drnevich ★ 2.0k
0
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0
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970
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intron coordination and annotation
ChIPSeq
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
0
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0
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1.0k
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.6 years ago xubeisi • 0
0
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1
reply
904
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.7 years ago by ★ 1.3k • written 2.7 years ago by • 0
0
votes
3
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1.4k
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
0
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0
replies
901
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.8 years ago Swadha • 0
0
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1
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1.1k
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 2.8 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
vote
2
replies
1.7k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by • 0
1
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1
reply
1.3k
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 3.1 years ago by ★ 5.2k • written 3.1 years ago by • 0
0
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0
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980
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
3.2 years ago Nadav • 0
0
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0
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1.1k
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DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
3.3 years ago Drew • 0
0
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6
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2.4k
views
cel files with affy library
ChIPSeq
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
3
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12
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4.3k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 3.5 years ago by ★ 5.2k • written 5.4 years ago by ▴ 20
0
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2
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1.5k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
3.5 years ago maria.soler • 0
2
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3
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1.9k
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 3.4 years ago by ▴ 20 • written 3.5 years ago by • 0
5
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8
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2.8k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 2.7 years ago by ▴ 20 • written 3.6 years ago by ▴ 30
0
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1
reply
2.2k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3.7 years ago by 67k • written 3.7 years ago by ▴ 290
2
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5
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4.6k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 2.1 years ago by • 0 • written 3.7 years ago by ★ 5.2k
2
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4
replies
1.6k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.7 years ago richardallenfriedmanbrooklyn ▴ 30
0
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0
replies
2.0k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
3.9 years ago Goku • 0
2
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6
replies
1.8k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
3.9 years ago Goku • 0
0
votes
3
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1.3k
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 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
1
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4
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1.7k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
4.0 years ago • updated 3.9 years ago SFn • 0
0
votes
11
replies
2.4k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.0 years ago by • 0 • written 4.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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