Showing : ChipSeq • reset
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88
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
13 days ago yvonneh • 0
0
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1
reply
128
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what is the sampleFiles
chipseq
updated 29 days ago by 65k • written 29 days ago by • 0
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0
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188
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Best method for annotating distal peaks
ChIPSeq annotation ChIPpeakAnno
3 months ago nilanjanamani88 • 0
1
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3
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423
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 3 months ago by 42k • written 3 months ago by • 0
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0
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182
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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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1.9k
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DiffBind error: diffbind DESeq2 analysis has not been run for this contrast
DiffBind R chipseq
updated 5 months ago by ★ 5.2k • written 6.6 years ago by • 0
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0
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342
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Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
csaw ChIPseq DiffBind
6 months ago jared.andrews07 ▴ 30
1
vote
1
reply
466
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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 7 months ago by 65k • written 7 months ago by • 0
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0
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294
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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
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14
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1.2k
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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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3.2k
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
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1.2k
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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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623
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annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 12 months ago by ▴ 70 • written 13 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 13 months ago by ▴ 10
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2
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1.1k
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
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0
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456
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
13 months ago Giulia • 0
1
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2
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1.1k
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
14 months ago chavaleab • 0
2
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4
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3.4k
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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
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707
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
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How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
16 months ago stacy.genovese • 0
2
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5
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3.4k
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
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2
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788
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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
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1
reply
881
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DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 19 months ago by ★ 5.2k • written 19 months ago by • 0
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 21 months ago by ▴ 40 • written 4.1 years ago by ▴ 10
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1
reply
911
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
22 months ago • updated 21 months ago Jenny Drnevich ★ 2.0k
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0
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704
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intron coordination and annotation
ChIPSeq
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
0
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0
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816
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
23 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
718
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 2.0 years ago by ★ 1.3k • written 2.0 years 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 2.0 years ago by ★ 5.2k • written 2.0 years ago by • 0
0
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0
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699
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
877
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 2.2 years ago by ★ 5.2k • written 2.2 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
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0
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748
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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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911
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 2.8 years ago by • 0 • written 2.8 years ago by • 0
3
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12
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3.4k
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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1.1k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.8 years ago maria.soler • 0
2
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4
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1.2k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
3.0 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 3.0 years ago by 65k • written 3.0 years ago by ▴ 290
2
votes
3
replies
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 6.1 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
1.4k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
3.3 years ago • updated 3.2 years ago SFn • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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