Showing : differential binding analysis • reset
3
votes
2
replies
1.4k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 5.5 years ago by ★ 5.2k • written 5.5 years ago by • 0
0
votes
3
replies
1.0k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
1
vote
3
replies
1.4k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 3.5 years ago by ★ 5.2k • written 5.7 years ago by ▴ 10
4
votes
7
replies
2.6k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 20
4
votes
6
replies
1.5k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 60
2
votes
10
replies
3.3k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 60
2
votes
4
replies
1.8k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.3 years ago by ★ 3.7k • written 6.3 years ago by ▴ 60
2
votes
4
replies
1.4k
views
DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
0
votes
1
reply
807
views
Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 6.3 years ago by ★ 5.2k • written 6.3 years ago by • 0
2
votes
5
replies
1.3k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
2
votes
4
replies
1.1k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by • 0
4
votes
3
replies
1.2k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 60
9
votes
17
replies
1.8k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
6.4 years ago Hesh ▴ 10
4
votes
7
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1.4k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 60
2
votes
2
replies
820
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 6.4 years ago by ★ 5.2k • written 6.4 years ago by ▴ 60
4
votes
7
replies
1.4k
views
Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 60
1
vote
2
replies
784
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 6.5 years ago by 65k • written 6.5 years ago by ▴ 60
2
votes
1
reply
1.1k
views
Receiving error trying to import matrix into DESeq2
deseq2 deseq differential binding analysis
updated 6.5 years ago by ▴ 60 • written 6.5 years ago by ▴ 60
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.6 years ago by ▴ 30
3
votes
3
replies
1.6k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
5
votes
7
replies
4.5k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
7.1 years ago BioinfGuru ▴ 30
3
votes
9
replies
3.5k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by ▴ 60
3
votes
6
replies
1.9k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
0
votes
3
replies
1.3k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
2
votes
1
reply
2.0k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 7.9 years ago by ★ 5.2k • written 7.9 years ago by • 0
4
votes
1
reply
2.8k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ★ 7.9k
1
vote
1
reply
1.6k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 10
4
votes
2
replies
1.4k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
8.5 years ago Pierre-François Roux • 0
1
vote
6
replies
5.8k
views
question about DiffBind
DiffBind differential binding analysis
updated 8.6 years ago by ★ 5.2k • written 8.7 years ago by • 0
31 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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