Showing : ChIPseq • reset
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6
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cel files with affy library
ChIPSeq
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
3
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12
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611
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Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 5 weeks ago by ★ 4.1k • written 2.0 years ago by ▴ 20
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2
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150
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Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
7 weeks ago • updated 5 weeks ago maria.soler • 0
2
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3
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231
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An error using Diffbind plotprofile
ChIPSeq profileplyr DiffBind
updated 16 days ago by ▴ 20 • written 7 weeks ago by • 0
5
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7
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325
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how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
9 weeks ago • updated 8 weeks ago pegah.taklifi ▴ 30
0
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1
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213
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DiffBind Normalisation between Narrow/Broad Peaks from different peak callers
ChIPSeq SICER2 DiffBind MACS2 offtopic
updated 3 months ago by 58k • written 3 months ago by ▴ 240
1
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2
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296
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News: New in DiffBind 3.2: dba.plotProfile() - Peak profiles and profile heatmaps
profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq
3 months ago • updated 15 days ago Rory Stark ★ 4.1k
2
votes
4
replies
279
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could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
4 months ago • updated 3 months ago richardallenfriedmanbrooklyn • 0
0
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0
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201
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
5 months ago Goku • 0
2
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6
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323
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Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
5 months ago Goku • 0
0
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3
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243
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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 6 months ago by ▴ 150 • written 6 months ago by • 0
1
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4
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294
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
7 months ago • updated 6 months ago SFn • 0
0
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11
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540
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Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 7 months ago by • 0 • written 8 months ago by • 0
0
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2
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278
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DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
9 months ago indi97 • 0
0
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2
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669
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ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
10 months ago • updated 7 months ago Mar Mar • 0
1
vote
4
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954
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MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 10 months ago by ★ 4.1k • written 3.7 years ago by • 0
2
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4
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541
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 10 months ago by ★ 4.1k • written 22 months ago by ▴ 30
4
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3
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281
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 10 months ago by ★ 4.1k • written 22 months ago by ▴ 10
1
vote
3
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1.3k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 10 months ago by ★ 4.1k • written 3.5 years ago by ▴ 10
1
vote
8
replies
553
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
10 months ago Hesh • 0
1
vote
1
reply
557
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 10 months ago by ★ 4.1k
0
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1
reply
191
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 10 months ago by 58k • written 10 months ago by • 0
0
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1
reply
241
views
CHIPQC error regarding BiocParallel
CHIPQC Diffbind chipseq rory stark Thomas Carroll
updated 17 months ago by 25k • written 17 months ago by ▴ 10
1
vote
7
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266
views
DiffBind: dealing with replicates
diffbind chipseq
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
0
votes
1
reply
180
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Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 19 months ago by 58k • written 19 months ago by • 0
0
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1
reply
167
views
DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 19 months ago by ★ 4.1k • written 19 months ago by ▴ 10
0
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0
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166
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
22 months ago • updated 21 months ago researcher • 0
0
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0
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199
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
2.0 years ago laura.mannarino ▴ 20
0
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1
reply
208
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diffBind analysis: only one replicate
diffbind chipseq
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
1
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3
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393
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 2.2 years ago by 25k • written 2.2 years ago by ▴ 10
0
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5
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352
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process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
2.3 years ago Kath • 0
2
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2
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898
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DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
0
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3
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345
views
Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
0
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0
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620
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Error while annotating with Chipseeker
annotation chipseq
2.6 years ago hamaor • 0
0
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0
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522
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
2.7 years ago bioinfouser2 ▴ 10
3
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7
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1.4k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 2.7 years ago by 34k • written 2.7 years ago by • 0
3
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2
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529
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by • 0
3
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4
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825
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ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 3.0 years ago by 58k • written 3.0 years ago by • 0
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7
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578
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ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 3.0 years ago by ★ 1.2k • written 3.0 years ago by • 0
1
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3
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721
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How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 3.0 years ago by ★ 1.2k • written 3.1 years ago by ▴ 10
0
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0
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375
views
Cannot open file because of connection error
systemArgs chipseq working directory
3.1 years ago hallie.s • 0
0
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0
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453
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Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
3.1 years ago l.brown ▴ 10
0
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0
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458
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Error when runing exomePeak
exomePeak chipseq
3.2 years ago syrttgump ▴ 20
0
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0
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356
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error in plotting data with CompareCluster function
comparecluster chipseq
3.2 years ago Ashley • 0
1
vote
1
reply
408
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 3.3 years ago by ★ 4.1k • written 3.3 years ago by • 0
2
votes
3
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863
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 4 months ago by ★ 4.1k • written 3.4 years ago by ▴ 10
0
votes
1
reply
427
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 3.3 years ago by 58k • written 3.3 years ago by • 0
4
votes
7
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1.3k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 3.3 years ago by 34k • written 3.3 years ago by ▴ 20
0
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0
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437
views
Differential ChIP regions across >2 conditions
diffbind chipseq
3.4 years ago Shamaine • 0
2
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3
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2.2k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
3.4 years ago maria.kondili • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Comment: Issue::DesignPrimers DECIPHER by slwmartin • 0
Hey, I'm having this issue too. I've tried reinstalling using Conda a few times without luck. Did you reinstall with Conda or from the tar …
Comment: Log fold change interpretation of time series with Wald test by jd348 • 0
So would you recommend still using Log2fold change as a measurement for effect size?
Answer: Error in `*tmp*`$samples : $ operator is invalid for atomic vectors by James W. MacDonald 58k
I believe you want ``` > x <- as.matrix(read.delim("E:/bioinformatic/RNAseq/GSE168008_raw_count.txt", sep ="" ,row.names = 1)) > sampl…
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Awards • All
Teacher to Vincent J. Carey, Jr. 6.5k
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Scholar to Yang Liao ▴ 260
Scholar to James W. MacDonald 58k
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