Showing : ChIPseq • reset
2
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4
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1.9k
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
4.4 years ago • updated 4.3 years ago richardallenfriedmanbrooklyn ▴ 30
0
votes
0
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2.1k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4.5 years ago Goku • 0
2
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6
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2.1k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4.5 years ago Goku • 0
0
votes
3
replies
1.4k
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 4.5 years ago by ▴ 780 • written 4.5 years ago by • 0
1
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4
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2.0k
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
4.6 years ago • updated 4.5 years ago SFn • 0
0
votes
11
replies
2.8k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.6 years ago by • 0 • written 4.7 years ago by • 0
0
votes
2
replies
1.6k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
4.8 years ago indi97 • 0
2
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2
replies
3.0k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.9 years ago • updated 4.6 years ago Mar Mar ▴ 20
1
vote
4
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2.6k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 4.9 years ago by ★ 5.2k • written 7.7 years ago by • 0
2
votes
4
replies
2.3k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 4.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 40
4
votes
3
replies
1.5k
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 4.9 years ago by ★ 5.2k • written 5.9 years ago by ▴ 10
1
vote
3
replies
3.8k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 4.9 years ago by ★ 5.2k • written 7.6 years ago by ▴ 10
1
vote
9
replies
4.6k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 2.8 years ago by ▴ 670 • written 4.9 years ago by ▴ 10
1
vote
1
reply
2.1k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.9 years ago by ★ 5.2k
0
votes
1
reply
2.2k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
7
replies
3.6k
views
DiffBind: dealing with replicates
diffbind chipseq
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
votes
1
reply
1.3k
views
Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 5.6 years ago by 68k • written 5.6 years ago by • 0
0
votes
1
reply
1.2k
views
DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 5.6 years ago by ★ 5.2k • written 5.6 years ago by ▴ 10
0
votes
0
replies
772
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
5.8 years ago researcher • 0
0
votes
0
replies
1000
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
6.0 years ago laura.mannarino ▴ 20
0
votes
1
reply
1.8k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 2.4 years ago by • 0 • written 6.1 years ago by • 0
1
vote
3
replies
1.7k
views
Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 20
0
votes
5
replies
1.7k
views
process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
6.3 years ago Kath • 0
2
votes
2
replies
3.5k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
0
votes
3
replies
1.3k
views
Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
0
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0
replies
1.5k
views
Error while annotating with Chipseeker
annotation chipseq
6.6 years ago hamaor • 0
0
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0
replies
1.5k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.8 years ago bioinfouser2 ▴ 10
3
votes
7
replies
5.4k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
votes
2
replies
1.9k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 6.9 years ago by ★ 5.2k • written 6.9 years ago by • 0
3
votes
4
replies
3.5k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
votes
7
replies
2.2k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 7.0 years ago by ★ 1.3k • written 7.0 years ago by • 0
1
vote
3
replies
2.1k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 7.0 years ago by ★ 1.2k • written 7.1 years ago by ▴ 10
0
votes
0
replies
897
views
Cannot open file because of connection error
systemArgs chipseq working directory
7.1 years ago hallie.s • 0
0
votes
0
replies
1.4k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
7.1 years ago l.brown ▴ 10
0
votes
0
replies
1.0k
views
Error when runing exomePeak
exomePeak chipseq
7.2 years ago syrttgump ▴ 20
0
votes
0
replies
1.1k
views
error in plotting data with CompareCluster function
comparecluster chipseq
7.2 years ago Ashley • 0
1
vote
1
reply
970
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
2
votes
3
replies
3.5k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 4.4 years ago by ★ 5.2k • written 7.4 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 7.3 years ago by 68k • written 7.3 years ago by • 0
4
votes
7
replies
3.4k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 20
0
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0
replies
1.0k
views
Differential ChIP regions across >2 conditions
diffbind chipseq
7.4 years ago Shamaine • 0
3
votes
3
replies
5.1k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
7.4 years ago maria.kondili ▴ 10
1
vote
1
reply
2.2k
views
enrichGO (clusterProfiler) produces different results
chipseq go enrichment clusterprofiler
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by ▴ 840
2
votes
4
replies
2.0k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 7.7 years ago by ★ 11k • written 7.7 years ago by ▴ 20
1
vote
1
reply
2.3k
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 60
5
votes
7
replies
3.0k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 60
4
votes
3
replies
1.7k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 60
0
votes
0
replies
1.5k
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
7.8 years ago tyler.chukwu • 0
3
votes
7
replies
2.5k
views
dba.count with pre-defined regions
dba.count dba chipseq diffbind
updated 7.8 years ago by ★ 5.2k • written 7.8 years ago by ▴ 10
5
votes
6
replies
6.3k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.8 years ago Hesh ▴ 10
194 results • Page 2 of 4
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Comment: DiffBind - question on the use of filtered or unfiltered input data by deltaexecutor4 • 0
FFH4X is a [Free Fire mod][1] menu APK that offers cheats like auto headshot, aimbot, ESP, wallhack, and unlimited skins. Players use it to…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
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Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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