Showing : Chipseq • reset
2
votes
4
replies
2.1k
views
could not duplicate the fragment length in "Reads to Regions" csaw tutorial
chipseq csaw; crosscorrelation
4.7 years ago richardallenfriedmanbrooklyn ▴ 30
0
votes
0
replies
2.2k
views
Blacklist error at dba.analyze(dbObj)
DiffBind ChIPSeq
4.9 years ago Goku • 0
2
votes
6
replies
2.3k
views
Error with dba.count(dbObj) in DiffBind
DiffBind ChIPSeq
4.9 years ago Goku • 0
0
votes
3
replies
1.6k
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 4.9 years ago by ▴ 780 • written 4.9 years ago by • 0
1
vote
4
replies
2.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq DiffBind ExperimentalDesign
5.0 years ago • updated 4.9 years ago SFn • 0
0
votes
11
replies
3.1k
views
Problem in subtracting ChIP Seq experiment with the input using ChIPSeqSpike
chipseq ChIPSeqSpike
updated 5.0 years ago by • 0 • written 5.1 years ago by • 0
0
votes
2
replies
1.8k
views
DiffBind Error When using dba.count()
ChIP-Rx DiffBind chipseq
5.2 years ago indi97 • 0
2
votes
2
replies
3.2k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
5.2 years ago • updated 5.0 years ago Mar Mar ▴ 20
1
vote
4
replies
2.7k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5.2 years ago by ★ 5.2k • written 8.0 years ago by • 0
2
votes
4
replies
2.4k
views
Integrating the computed spike-in coefficients for the normalisation before differential peaks analysis
DiffBind Chipseq spike-ins
updated 5.2 years ago by ★ 5.2k • written 6.2 years ago by ▴ 40
4
votes
3
replies
1.6k
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 5.2 years ago by ★ 5.2k • written 6.3 years ago by ▴ 10
1
vote
3
replies
4.1k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 5.2 years ago by ★ 5.2k • written 7.9 years ago by ▴ 10
1
vote
9
replies
5.1k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 3.2 years ago by ▴ 670 • written 5.3 years ago by ▴ 10
1
vote
1
reply
2.4k
views
News: Extensive updates in DiffBind 3.0
Normalization ATACSeq ChIPSeq DiffBind chipseq
written 5.3 years ago by ★ 5.2k
0
votes
1
reply
2.3k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
1
vote
7
replies
3.9k
views
DiffBind: dealing with replicates
diffbind chipseq
updated 5.9 years ago by ★ 5.2k • written 5.9 years ago by • 0
0
votes
1
reply
1.5k
views
Retrieving ChIP-seq data from Geo database
ChIPseq GEO data base
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
1
reply
1.3k
views
DiffBind MA plot annotate promoter regions with different colour
diffbind chipseq rorystark
updated 6.0 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
0
votes
0
replies
835
views
How to change the text size for the names of ColAttributes
diffbind colattributes chipseq cex
6.2 years ago researcher • 0
0
votes
0
replies
1.1k
views
ChIPQC makes a neverending loop while using all chromosomes
chipqc chipseq ChIPQC
6.4 years ago laura.mannarino ▴ 20
0
votes
1
reply
1.9k
views
diffBind analysis: only one replicate
diffbind chipseq
updated 2.7 years ago by • 0 • written 6.4 years ago by • 0
1
vote
3
replies
1.8k
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 6.6 years ago by 25k • written 6.6 years ago by ▴ 20
0
votes
5
replies
1.9k
views
process bed/bedGraph files with the same coordinates for all the samples
ChIPSeq
6.6 years ago Kath • 0
2
votes
2
replies
3.8k
views
DiffBind's MA plots for ChIP-seq - how to properly interpret normalization from them?
diffbind R MAplot Chipseq
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Diffbind affinity based analysis
Diffbind ChIPseq Affinity analysis Differentially bound sites occupancy analysis
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by • 0
0
votes
0
replies
1.6k
views
Error while annotating with Chipseeker
annotation chipseq
6.9 years ago hamaor • 0
0
votes
0
replies
1.6k
views
How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
7.1 years ago bioinfouser2 ▴ 10
3
votes
7
replies
5.8k
views
DEseq2 for differential binding analysis ChIP seq
deseq2 diffbind csaw greylistchip chipseq
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
3
votes
2
replies
2.0k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 7.3 years ago by ★ 5.2k • written 7.3 years ago by • 0
3
votes
4
replies
3.7k
views
ChIPseeker/Question about ''annoatePeak' function and for Bioconductor AnnotationData Packages for L.japonicus
chipseeker Bioconductor AnnotationData Packages Lotus japonicus ChIPseq
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
0
votes
7
replies
2.3k
views
ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
chippeakanno chipseq R
updated 7.4 years ago by ★ 1.3k • written 7.4 years ago by • 0
1
vote
3
replies
2.3k
views
How to do functional enrichment analysis for only promoter regions using ChIPseeker
chipseeker chipseq
updated 7.4 years ago by ★ 1.2k • written 7.5 years ago by ▴ 10
0
votes
0
replies
955
views
Cannot open file because of connection error
systemArgs chipseq working directory
7.5 years ago hallie.s • 0
0
votes
0
replies
1.5k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
7.5 years ago l.brown ▴ 10
0
votes
0
replies
1.1k
views
Error when runing exomePeak
exomePeak chipseq
7.5 years ago syrttgump ▴ 20
0
votes
0
replies
1.2k
views
error in plotting data with CompareCluster function
comparecluster chipseq
7.5 years ago Ashley • 0
1
vote
1
reply
1.1k
views
getting DiffBind full result list
deseq2 diffbind chipseq
updated 7.7 years ago by ★ 5.2k • written 7.7 years ago by • 0
2
votes
3
replies
3.8k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 4.7 years ago by ★ 5.2k • written 7.8 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Reg.: Ringo,open source R package
agilent microarrays chipseq
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
4
votes
7
replies
3.7k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Differential ChIP regions across >2 conditions
diffbind chipseq
7.8 years ago Shamaine • 0
3
votes
3
replies
5.6k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
7.8 years ago maria.kondili ▴ 10
1
vote
1
reply
2.4k
views
enrichGO (clusterProfiler) produces different results
chipseq go enrichment clusterprofiler
updated 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 840
2
votes
4
replies
2.1k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 20
1
vote
1
reply
2.5k
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 60
5
votes
7
replies
3.2k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker chipseq chip
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by ▴ 60
4
votes
3
replies
1.8k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 60
0
votes
0
replies
1.6k
views
Job: Bioinformatics Analyst II/III - Banchereau Lab @ The Jackson Laboratory
rnaseq atac-seq iso-seq chipseq Job
8.1 years ago tyler.chukwu • 0
3
votes
7
replies
2.8k
views
dba.count with pre-defined regions
dba.count dba chipseq diffbind
updated 8.2 years ago by ★ 5.2k • written 8.2 years ago by ▴ 10
5
votes
6
replies
6.7k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
8.2 years ago Hesh ▴ 10
194 results • Page 2 of 4
Recent ...
Replies
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
Answer: Confused about the CPM and TMM normalization in edgeR
Awards • All
Teacher to Michael Love 43k
Supporter to fl ▴ 20
Popular Question to James W. MacDonald 68k
Popular Question to rcavalca ▴ 140
Popular Question to James Aiden • 0
Locations • All
The Netherlands, 3 minutes ago
Poland, 20 minutes ago
Chile, 33 minutes ago
United States, 40 minutes ago
United States, 48 minutes ago
Traffic: 1211 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6