Showing : ChipSeq • reset
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128
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
6 weeks ago yvonneh • 0
0
votes
1
reply
155
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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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259
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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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468
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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
0
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0
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215
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Parameter bSubControl with no effect in DiffBind dba.count?
bSubControl ChIPSeq DiffBind
5 months ago frueher • 0
0
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0
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383
views
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
519
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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323
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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
0
votes
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
vote
4
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1.1k
views
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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661
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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
15 months ago Giulia • 0
0
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0
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476
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
15 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
vote
3
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741
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
16 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
913
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
replies
1.4k
views
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
933
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
0
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0
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728
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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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860
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
2.0 years ago xubeisi • 0
0
votes
1
reply
742
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
replies
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
724
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
900
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
replies
1.3k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 2.3 years ago by ★ 5.2k • written 2.3 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
votes
0
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775
views
findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
2.5 years ago Nadav • 0
0
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0
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937
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
replies
1.8k
views
cel files with affy library
ChIPSeq
updated 2.8 years ago by • 0 • written 2.9 years ago by • 0
3
votes
12
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3.6k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.9 years ago by ★ 5.2k • written 4.8 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 maria.soler • 0
2
votes
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
votes
4
replies
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
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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
replies
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
2.1k
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: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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