Showing : ChipSeq • reset
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Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4.4 years ago Goku • 0
2
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6
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2.1k
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4.5 years ago • updated 4.4 years ago Goku • 0
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3
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1.4k
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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
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11
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2.8k
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.6 years ago by • 0 • written 4.6 years ago by • 0
0
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2
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1.6k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
4.8 years ago • updated 4.7 years ago indi97 • 0
2
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2
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3.0k
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.8 years ago • updated 4.6 years ago Mar Mar ▴ 20
1
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4
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2.5k
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MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 4.8 years ago by ★ 5.2k • written 7.6 years ago by • 0
2
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4
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2.2k
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Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 4.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 40
4
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3
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1.5k
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Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 4.8 years ago by ★ 5.2k • written 5.8 years ago by ▴ 10
1
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3
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3.8k
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Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 4.8 years ago by ★ 5.2k • written 7.5 years ago by ▴ 10
1
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9
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4.5k
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Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 2.8 years ago by ▴ 670 • written 4.8 years ago by ▴ 10
1
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1
reply
2.1k
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News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 4.8 years ago by ★ 5.2k
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1
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2.2k
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How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
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7
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3.6k
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DiffBind: dealing with replicates
diffbind chipseq
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
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1
reply
1.3k
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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1
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1.2k
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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
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0
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764
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How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
5.8 years ago • updated 5.7 years ago researcher • 0
0
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0
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989
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ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
6.0 years ago laura.mannarino ▴ 20
0
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1
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1.8k
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diffBind analysis: only one replicate
diffbind chipseq
updated 2.3 years ago by • 0 • written 6.0 years ago by • 0
1
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3
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1.6k
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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
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5
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1.7k
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
6.2 years ago Kath • 0
2
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2
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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
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3
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1.3k
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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
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1.5k
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Error while annotating with Chipseeker
annotation chipseq
6.5 years ago hamaor • 0
0
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0
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1.5k
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.7 years ago bioinfouser2 ▴ 10
3
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7
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5.3k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
3
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2
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1.8k
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diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 6.8 years ago by ★ 5.2k • written 6.9 years ago by • 0
3
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4
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3.5k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
0
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7
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2.1k
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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
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3
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2.0k
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
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0
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894
views
Cannot open file because of connection error
systemArgs chipseq working directory
7.1 years ago hallie.s • 0
0
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0
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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
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0
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1.0k
views
Error when runing exomePeak
exomePeak chipseq
7.1 years ago syrttgump ▴ 20
0
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0
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1.1k
views
error in plotting data with CompareCluster function
comparecluster chipseq
7.1 years ago Ashley • 0
1
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1
reply
964
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by • 0
2
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3
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3.5k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 4.3 years ago by ★ 5.2k • written 7.4 years ago by ▴ 10
0
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1
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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
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7
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3.4k
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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
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1.0k
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Differential ChIP regions across >2 conditions
diffbind chipseq
7.4 years ago Shamaine • 0
3
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3
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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
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1
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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
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4
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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 7.6 years ago by ★ 11k • written 7.6 years ago by ▴ 20
1
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1
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2.3k
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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
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7
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2.9k
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ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 60
4
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3
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1.6k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 60
0
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0
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1.5k
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
7.7 years ago tyler.chukwu • 0
3
votes
7
replies
2.5k
views
dba.count with pre-defined regions
dba.count dba chipseq diffbind
updated 7.7 years ago by ★ 5.2k • written 7.7 years ago by ▴ 10
5
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6
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6.3k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.8 years ago Hesh ▴ 10
0
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1
reply
3.0k
views
how to define the downstream range in ChIPseeker
ChIPseeker H3K27me3 chipseq chipseeker
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 10
194 results • Page 2 of 4
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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