Showing : ChipSeq • reset
3
votes
9
replies
4.1k
views
ChIPQC and broadPeak input
chipseq chipqc chip-seq
10.5 years ago lindahove ▴ 10
5
votes
6
replies
6.8k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
8.3 years ago Hesh ▴ 10
2
votes
6
replies
3.3k
views
ChIPseeker: covplot function: error with some ENCODE data sets
chiPseeker covplot ENCODE ChIpseq
10.9 years ago • updated 10.8 years ago sarabusquets88 • 0
5
votes
5
replies
2.7k
views
Metagenomic analysis: Aligning ChIPseq data on TSS
metagenomics chipseq biomart shortread convert biomaRt
11.5 years ago patrick.schordert ▴ 30
27
votes
22
replies
23k
views
DESeq2 for ChIP-seq differential peaks
deseq2 deseq chipseq
updated 8.7 years ago by ▴ 120 • written 10.5 years ago by ▴ 200
1
vote
4
replies
2.7k
views
MAnorm output as DiffBind input.
MAnorm diffbind normalization chipseq
updated 5.3 years ago by ★ 5.3k • written 8.1 years ago by • 0
3
votes
12
replies
5.5k
views
Is it possible to change how DiffBind merge peaks?
DiffBind ChIPseq
updated 4.6 years ago by ★ 5.3k • written 6.5 years ago by ▴ 20
7
votes
11
replies
6.7k
views
annotatePeak() in ChIPseeker - how long does it take to run?
annotatePeak chipseeker chipseq org.Mm.eg.db TxDb.Mmusculus.UCSC.mm9.knownGene
updated 10.4 years ago by 25k • written 10.6 years ago by • 0
0
votes
3
replies
2.4k
views
Problem with rGADEM & MotIV - one matrix consensus after GADEM() and one plot enrichment motif
rgadem motiv chipseq jaspar
updated 10.8 years ago by • 0 • written 10.8 years ago by • 0
8
votes
9
replies
7.6k
views
ChIPseq-style peak calling for paired-end sequencing?
Chipseq DNAseq ATAC bayespeak narrowpeaks
updated 10.8 years ago by 53k • written 10.8 years ago by ▴ 140
2
votes
4
replies
2.2k
views
R package for Meta-Analysis of CHIP-Seq data
chipseq meta-analysis ubuntu
8.8 years ago rezapanahi222 • 0
0
votes
6
replies
2.5k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO rtracklayer CAMERA chipseq Gviz ChIPSeq GO rtracklayer CAMERA chipseq Gviz
updated 12.8 years ago by ▴ 750 • written 12.9 years ago by ★ 13k
0
votes
2
replies
1.9k
views
Extracting overlapping gene names from a list of peaks
ChIPSeq chipseq ChIPSeq chipseq
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ▴ 20
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 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 60
0
votes
6
replies
3.3k
views
cel files with affy library
ChIPSeq
updated 4.6 years ago by • 0 • written 4.6 years ago by • 0
6
votes
5
replies
2.4k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.6 years ago by ▴ 30
0
votes
2
replies
1.3k
views
mypeaklist in ChIPpeakAnno
ChIPSeq chipseq ChIPSeq chipseq
15.6 years ago • updated 15.5 years ago Julie Zhu ★ 4.3k
5
votes
8
replies
2.0k
views
Help with error install csaw
ChIPSeq ATACSeq
written 2.9 years ago by ▴ 20
1
vote
3
replies
4.3k
views
Downsampling ChIP-seq BAM files with spike in normalization factor before feeding into Diffbind
diffbind chipseq chipqc
updated 5.3 years ago by ★ 5.3k • written 8.0 years ago by ▴ 10
3
votes
7
replies
2.8k
views
dba.count with pre-defined regions
dba.count dba chipseq diffbind
updated 8.2 years ago by ★ 5.3k • written 8.2 years ago by ▴ 10
3
votes
4
replies
3.8k
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
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 5.3 years ago by ★ 5.3k • written 6.3 years ago by ▴ 40
3
votes
3
replies
5.7k
views
Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
diffbind chipseq peaks dba is.na
7.9 years ago maria.kondili ▴ 10
5
votes
8
replies
3.5k
views
how to construct a DBA object from count matrix
ChIPSeq ATACSeq differentially_occupied DiffBind
updated 3.7 years ago by ▴ 20 • written 4.6 years ago by ▴ 30
0
votes
3
replies
4.5k
views
unknown error in DiffBind package
ChIPSeq chipseq DiffBind ChIPSeq chipseq DiffBind
updated 11.9 years ago by ★ 5.3k • written 11.9 years ago by ★ 13k
2
votes
3
replies
3.0k
views
MA plot DiffBind in ggplot2
diffbind ggplot2 r chipseq
updated 8.4 years ago by ★ 5.3k • written 8.5 years ago by • 0
0
votes
2
replies
1.8k
views
chip-seq data analysis
Transcription ChIPSeq Alignment chipseq Transcription ChIPSeq Alignment chipseq
updated 16.0 years ago by 21k • written 16.0 years ago by ▴ 60
2
votes
3
replies
3.8k
views
ChIPseeker peak annotation tssRegion
chipseeker annotation chipseq
8.3 years ago lifeng.liu.biology ▴ 10
2
votes
4
replies
4.3k
views
Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
chipseq deseq2 htseqcounts
updated 3.0 years ago by ▴ 10 • written 9.0 years ago by ▴ 40
0
votes
2
replies
2.5k
views
Diffbind: Peak score normalization
normalization chipseq diffbind
11.1 years ago medinaale • 0
0
votes
7
replies
2.3k
views
DiffBind fails to derive consensus peaksets
software error chipseq diffbind
updated 10.8 years ago by ▴ 670 • written 10.8 years ago by ▴ 320
3
votes
2
replies
3.1k
views
DiffBind "no lines available in input" error
diffbind chipseq
updated 9.6 years ago by ★ 5.3k • written 9.6 years ago by ▴ 50
6
votes
6
replies
4.2k
views
Score column for DiffBind::dba.peakset
DiffBind chipseq
updated 10.9 years ago by ▴ 670 • written 10.9 years ago by • 0
1
vote
7
replies
3.5k
views
loading dba.plotVolcano in DiffBind
diffbind chipseq atac-seq rory stark
updated 8.9 years ago by ★ 5.3k • written 8.9 years ago by • 0
2
votes
6
replies
2.2k
views
DiffBind for Allele-specific binding analysis
diffbind chipseq
updated 10.8 years ago by ★ 5.3k • written 10.8 years ago by ▴ 100
0
votes
5
replies
7.5k
views
diffbind
DiffBind chipseq
updated 2.6 years ago by ★ 5.3k • written 2.6 years ago by • 0
0
votes
1
reply
2.0k
views
IdeogramTrack and bigWig file errors in Gviz
ChIPSeq GO Network rtracklayer CAMERA chipseq Gviz ChIPSeq GO Network rtracklayer Gviz
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 40
0
votes
1
reply
1.1k
views
"islands" and number of reads in the island in package chipseq/ShortRead
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
updated 16.3 years ago by ★ 6.5k • written 16.3 years ago by ▴ 40
1
vote
3
replies
1.9k
views
DiffBind Error when dba.count on a pre-defined peak set
diffbind chipseq
updated 9.4 years ago by ★ 5.3k • written 9.4 years ago by ▴ 200
0
votes
1
reply
3.6k
views
merge error: 'by.x' and 'by.y' specify different numbers of columns
ChIPSeq biomaRt chipseq ChIPSeq biomaRt chipseq
updated 11.7 years ago by 68k • written 11.7 years ago by ▴ 50
0
votes
2
replies
1.6k
views
ChIPpeakAnno - VennDiagram P-value - NaN
ChIPSeq chipseq ChIPpeakAnno ChIPSeq chipseq ChIPpeakAnno
15.5 years ago Julie Zhu ★ 4.3k
1
vote
2
replies
1.4k
views
Providing specific regions to Diffbind
diffbind chipseq
updated 9.3 years ago by ★ 5.3k • written 9.3 years ago by • 0
0
votes
10
replies
2.3k
views
DESeq on CCAT identified chipseq peaks
ChIPSeq chipseq DESeq ChIPSeq chipseq DESeq
updated 11.8 years ago by ★ 5.3k • written 11.8 years ago by ★ 13k
0
votes
1
reply
1.4k
views
Involve tag count information in coverage function (IRanges, chipseq package)?
ChIPSeq Coverage chipseq ChIPSeq Coverage chipseq
15.5 years ago Xiaohui Wu ▴ 280
0
votes
1
reply
1.4k
views
How to install chipseq package
ChIPSeq chipseq ChIPSeq chipseq
updated 17.0 years ago by ★ 1.6k • written 17.0 years ago by ▴ 90
0
votes
3
replies
2.2k
views
Error in ChIPQC
chipseq ChIPQ
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 10
4
votes
2
replies
2.2k
views
Confusing error when running ChIPQC
chipqc chipseq
updated 10.4 years ago by ▴ 420 • written 10.4 years ago by ★ 7.9k
1
vote
2
replies
1.8k
views
question regarding custom normalizationFactors in DESeq2
deseq2 R chipseq normalization
updated 9.5 years ago by ★ 3.8k • written 9.5 years ago by • 0
0
votes
1
reply
1.9k
views
DiffBind loading Problem
Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind
12.1 years ago Rory Stark ★ 5.3k
0
votes
1
reply
1.3k
views
Gviz error after updating R
software error Gviz chipseq rnaseq
9.4 years ago ta_awwad ▴ 10
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
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