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 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
4.6 years ago • updated 4.5 years ago Goku • 0
0
votes
3
replies
1.5k
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 4.6 years ago by ▴ 780 • written 4.6 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
4.7 years ago • updated 4.6 years ago SFn • 0
0
votes
11
replies
2.9k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 4.7 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
4.9 years ago • updated 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 4.7 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
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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
3.9k
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 2.9 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 5.6 years ago by ★ 5.2k • written 5.6 years ago by • 0
0
votes
1
reply
1.4k
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 5.7 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
0
votes
0
replies
773
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
5.9 years ago • updated 5.8 years ago researcher • 0
0
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0
replies
1.0k
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
6.1 years ago laura.mannarino ▴ 20
0
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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
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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 6.3 years ago by 25k • written 6.3 years ago by ▴ 20
0
votes
5
replies
1.8k
views
process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
6.3 years ago Kath • 0
2
votes
2
replies
3.6k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.4 years ago by ★ 5.2k • written 6.4 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 6.4 years ago by ★ 5.2k • written 6.4 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
votes
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 7.0 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 7.1 years ago by ★ 1.3k • written 7.1 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 7.1 years ago by ★ 1.2k • written 7.2 years ago by ▴ 10
0
votes
0
replies
904
views
Cannot open file because of connection error
systemArgs chipseq working directory
7.2 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
7.2 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
982
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
3.6k
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 7.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
4
votes
7
replies
3.5k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
0
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0
replies
1.0k
views
Differential ChIP regions across >2 conditions
diffbind chipseq
7.5 years ago Shamaine • 0
3
votes
3
replies
5.2k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
7.5 years ago maria.kondili ▴ 10
1
vote
1
reply
2.2k
views
enrichGO (clusterProfiler) produces different results
chipseq go enrichment clusterprofiler
updated 7.6 years ago by ★ 1.2k • written 7.6 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 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 60
5
votes
7
replies
3.0k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 7.8 years ago by ★ 1.2k • written 7.8 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
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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
6.4k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
7.9 years ago Hesh ▴ 10
194 results • Page 2 of 4
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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