Showing : differential binding analysis • reset
4
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5
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1.9k
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Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.8 years ago by ▴ 30
1
vote
3
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1.6k
views
Is there a way to run Diffbind without the normalization ?
diffbind differential binding analysis
updated 3.7 years ago by ★ 5.2k • written 6.0 years ago by ▴ 10
3
votes
2
replies
1.4k
views
diffbind finding not differential site
diffbind chipseq histone chip-seq differential binding analysis
updated 5.7 years ago by ★ 5.2k • written 5.8 years ago by • 0
0
votes
3
replies
1.1k
views
DESeq2 group comparison
deseq2 deseq differential binding analysis
updated 5.8 years ago by 42k • written 5.8 years ago by ▴ 60
4
votes
7
replies
2.7k
views
Differential ChIP-Seq Analysis with DESeq2
chipseq deseq2 featurecounts differential binding analysis
updated 6.2 years ago by 42k • written 6.2 years ago by ▴ 20
4
votes
6
replies
1.7k
views
DESeq2 design and stats question
deseq2 differential binding analysis deseq atac-seq
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 60
0
votes
1
reply
860
views
Diffbind: How to compare the DBs called with and without a blocking factor
diffbind differential binding analysis blocking
updated 6.5 years ago by ★ 5.2k • written 6.6 years ago by • 0
2
votes
4
replies
1.5k
views
DiffBind report and MA-plot DB difference
diffbind differential binding analysis R report
updated 6.5 years ago by ★ 5.2k • written 6.5 years ago by • 0
2
votes
10
replies
3.6k
views
DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 6.5 years ago by 42k • written 6.5 years ago by ▴ 60
2
votes
4
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2.0k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.5 years ago by ★ 3.7k • written 6.5 years ago by ▴ 60
2
votes
5
replies
1.4k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 60
2
votes
4
replies
1.2k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 6.6 years ago by ★ 5.2k • written 6.6 years ago by • 0
4
votes
3
replies
1.3k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 60
9
votes
17
replies
1.9k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 60
5
votes
6
replies
4.7k
views
Analyzing data without replicates using DiffBind
diffbind bioconductor differential binding analysis without replicate chipseq
6.7 years ago Hesh ▴ 10
4
votes
7
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1.5k
views
Filtering DESeq2 result export along multiple lines
deseq2 differential binding analysis deseq
updated 6.7 years ago by 42k • written 6.7 years ago by ▴ 60
2
votes
2
replies
860
views
Cleaning up DiffBind counts in relation to chromosome map
diffbind chipseq differential binding analysis
updated 6.7 years ago by ★ 5.2k • written 6.7 years ago by ▴ 60
4
votes
7
replies
1.5k
views
Altering design following DESeqDataSetFromMatrix and DESeq
deseq2 differential binding analysis
updated 6.7 years ago by 42k • written 6.7 years ago by ▴ 60
1
vote
2
replies
830
views
Pre-filtering DESeqDataSetFromMatrix input
deseq2 differential binding analysis
updated 6.7 years ago by 66k • written 6.7 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 6.8 years ago by ▴ 60 • written 6.8 years ago by ▴ 60
3
votes
3
replies
1.7k
views
csaw: how does unequal sample size affect filtering filterWindows step
csaw differential binding analysis sample size independent filtering statistical power
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
5
votes
7
replies
4.7k
views
Differential binding of ATAC-seq data with no replicates
ATAC differential binding analysis no replicates DEseq2 chromatin
7.4 years ago • updated 7.3 years ago BioinfGuru ▴ 30
3
votes
9
replies
3.8k
views
DiffBind BED output with score
diffbind differential binding analysis
updated 7.5 years ago by ★ 5.2k • written 7.5 years ago by ▴ 60
3
votes
6
replies
2.0k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
0
votes
3
replies
1.4k
views
Chip-seq analysis with input
chip-seq differential binding analysis
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
2
votes
1
reply
2.1k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind p-value differential binding analysis fold enrichment values using diffbind
updated 8.1 years ago by ★ 5.2k • written 8.1 years ago by • 0
4
votes
1
reply
2.9k
views
csaw - workflow to incorporate input/control samples?
csaw chipseq differential binding analysis
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 10
2
votes
1
reply
1.4k
views
Strategy for choosing window size and read extension length for csaw?
csaw differential binding analysis bin size
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ★ 7.9k
1
vote
1
reply
1.7k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 10
4
votes
2
replies
1.5k
views
Csaw : filter windows based on matched negative control
csaw differential binding analysis
8.8 years ago Pierre-François Roux • 0
1
vote
6
replies
5.9k
views
question about DiffBind
DiffBind differential binding analysis
updated 8.9 years ago by ★ 5.2k • written 8.9 years ago by • 0
31 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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