Showing : chipseq • reset
2
votes
14
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457
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ChIPpeakAnno: S.lycopersicum annotation missing
ChIPpeakAnno ChIPSeq
updated 28 days ago by 63k • written 4 weeks ago by ▴ 10
0
votes
5
replies
359
views
diffbind
DiffBind chipseq
updated 8 weeks ago by ★ 5.0k • written 8 weeks ago by • 0
1
vote
4
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463
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DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-change
ChIPSeq DiffBind
updated 3 months ago by ★ 5.0k • written 4 months ago by • 0
0
votes
2
replies
297
views
annotate peaks using a custom genome
ChIPSeq annotate ChIPpeakAnno
updated 4 months ago by ▴ 70 • written 5 months ago by ▴ 140
5
votes
8
replies
565
views
Help with error install csaw
ChIPSeq ATACSeq
updated 5 months ago by • 0 • written 5 months ago by • 0
0
votes
2
replies
513
views
DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
6 months ago Giulia • 0
0
votes
0
replies
208
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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?
DESeq2 ChIPSeq DiffBind edgeR HistoneModification
6 months ago Giulia • 0
1
vote
2
replies
460
views
how i can get the name of genes in pathway?
chipseq ChIPseeker
6 months ago chavaleab • 0
1
vote
3
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336
views
Only getting 10 peaks from mac2 callpeak
ChIPSeq
7 months ago stacy.genovese • 0
1
vote
4
replies
640
views
How to search a .narrowPeak file for a list of specific genes using GenomicRanges package
ChIPSeq PeakDetection
8 months ago stacy.genovese • 0
0
votes
2
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438
views
New to ChipSeq getting 0 peaks using dba()
ChipSeq ChIPSeqData chipseqDB
10 months ago • updated 9 months ago stacy.genovese • 0
0
votes
1
reply
575
views
DiffBind question _ SampleSheet / Venn diagram issue
chipseq DiffBind
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
6
votes
3
replies
860
views
MEDIPS for chIP-Seq
ChIPSeq
written 13 months ago by ▴ 30
0
votes
7
replies
1.3k
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 13 months ago by ▴ 40 • written 3.4 years ago by ▴ 10
0
votes
1
reply
613
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
14 months ago • updated 13 months ago Jenny Drnevich ★ 2.0k
0
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0
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438
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intron coordination and annotation
ChIPSeq
updated 14 months ago by ★ 3.4k • written 14 months ago by • 0
0
votes
0
replies
527
views
Job: Bioinformatics Research Scientist- Epigenetics Group
HiC Epigenetics HiCHIP ChIPSeq
15 months ago xubeisi • 0
0
votes
1
reply
469
views
AssignChromosomeRegion not working in Rstudio 4.2
ChIPpeakAnno ChIPSeq
updated 16 months ago by ★ 1.3k • written 16 months ago by • 0
0
votes
3
replies
685
views
DiffBind on static peak set for all samples
ChIPSeq DiffBind
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
0
votes
0
replies
449
views
Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
17 months ago Swadha • 0
0
votes
1
reply
579
views
Input peak set for DiffBind should be all peaks or FDR filtered?
ChIPSeq DiffBind
updated 17 months ago by ★ 5.0k • written 18 months ago by • 0
1
vote
2
replies
890
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
1
vote
1
reply
709
views
DiffBind scoreCol value question
DiffBind ChIPSeq chipseq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
0
replies
538
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findOverlapsOfPeaks - peaklist of connectedPeaks="min:
findOverlapsOfPeaks ChIPpeakAnno chipseq
21 months ago Nadav • 0
0
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0
replies
688
views
DiffBind spike-in normalisation with varying amounts of spike-in chromatin
DiffBind ChIPSeq Normalization SpikeIn
23 months ago Drew • 0
0
votes
6
replies
1.2k
views
cel files with affy library
ChIPSeq
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
3
votes
12
replies
2.5k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 2.1 years ago by ★ 5.0k • written 4.0 years ago by ▴ 20
0
votes
2
replies
847
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
2.2 years ago • updated 2.1 years ago maria.soler • 0
2
votes
3
replies
941
views
An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 2.1 years ago by ▴ 20 • written 2.2 years ago by • 0
5
votes
8
replies
1.6k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 15 months ago by ▴ 20 • written 2.2 years ago by ▴ 30
0
votes
1
reply
1.4k
views
DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 2.3 years ago by 63k • written 2.3 years ago by ▴ 270
2
votes
5
replies
2.4k
views
News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
updated 9 months ago by • 0 • written 2.3 years ago by ★ 5.0k
2
votes
4
replies
923
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
2.4 years ago • updated 2.3 years ago richardallenfriedmanbrooklyn • 0
0
votes
0
replies
1.4k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
2.5 years ago Goku • 0
2
votes
6
replies
1.1k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
2.5 years ago Goku • 0
0
votes
3
replies
776
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 2.5 years ago by ▴ 720 • written 2.5 years ago by • 0
1
vote
4
replies
990
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
2.6 years ago • updated 2.5 years ago SFn • 0
0
votes
11
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1.5k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 2.6 years ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
792
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
2.8 years ago indi97 • 0
2
votes
2
replies
2.0k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
2.9 years ago • updated 2.6 years ago Mar Mar ▴ 20
1
vote
4
replies
1.6k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 2.9 years ago by ★ 5.0k • written 5.7 years ago by • 0
2
votes
4
replies
1.5k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 2.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 40
4
votes
3
replies
735
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 2.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 10
1
vote
3
replies
2.3k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 2.9 years ago by ★ 5.0k • written 5.6 years ago by ▴ 10
1
vote
9
replies
2.2k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 9 months ago by ▴ 660 • written 2.9 years ago by ▴ 10
1
vote
1
reply
1.3k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 2.9 years ago by ★ 5.0k
0
votes
1
reply
1.1k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 2.9 years ago by 63k • written 2.9 years ago by • 0
1
vote
7
replies
1.7k
views
DiffBind: dealing with replicates
diffbind chipseq
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
votes
1
reply
723
views
Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 3.6 years ago by 63k • written 3.6 years ago by • 0
0
votes
1
reply
620
views
DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: List of Deprecated Packages for Bioc3.18 by Hervé Pagès 16k
Also the source package is not available [in BioC 3.17](https://bioconductor.org/packages/3.17/CancerInSilico) which means that the package…
Answer: DelayedArray::read_sparse_block by Hervé Pagès 16k
Hi Koki, Sorry again for the slow response. `read_sparse_block()` has been around for years. It's a generic function defined in the *…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Votes
Comment: NPARC package y-variable
Comment: List of Deprecated Packages for Bioc3.18
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
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