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Showing top results for tag: diffbind • reset
1
vote
9
replies
3.6k
views
8 follow
Bam files not accepted in dba.count
samtools diffbind dba.count bam
updated 4 days ago by • 0 • written 3.7 years ago by • 0
0
votes
0
replies
140
views
How to obtain shared peaks in DiffBind?
DiffBind ChIP-seq
10 days ago by Thomas • 0
3
votes
3
replies
406
views
How to make DiffBind Run Faster?
DiffBind ATAC-seq
updated 15 days ago by ★ 18k • written 21 days ago by ▴ 10
0
votes
0
replies
191
views
DiffBind ProfilePlot Having High Wide High Signals
DiffBind ATAC-seq
26 days ago by B.N. ▴ 10
0
votes
0
replies
214
views
DiffBind Profile Plot Error
DiffBind ATAC-seq
updated 29 days ago by 146k • written 29 days ago by ▴ 10
0
votes
1
reply
204
views
DiffBind count function error related with BiocParallel and IRanges
dba chipseq iranges diffbind
4 weeks ago by buffealo ▴ 130
6
votes
7
replies
523
views
Trying to understand basic DiffBind usage
DiffBind ChIP-seq
7 weeks ago by alejandrocastillaibeas ▴ 20
0
votes
0
replies
222
views
DiffBind for MBD-seq
DiffBind MBD-seq
9 weeks ago by mariannapauletto ▴ 90
0
votes
1
reply
175
views
Contrasting multiple tissues in DiffBind
DiffBind ChIP-seq
updated 11 weeks ago by 44k • written 11 weeks ago by • 0
1
vote
2
replies
372
views
How to use Diffbind to quantify signal in a set of custom peaks
atac-seq Diffbind
11 weeks ago by enanoide • 0
0
votes
0
replies
219
views
Diffbind: creating an affinity heatmap for clustering
Diffbind
3 months ago by BT • 0
2
votes
10
replies
847
views
CutNtag normalization without spike in
cutNtag csaw ChIPseq diffBind
4 months ago by gamma.jian ▴ 40
4
votes
2
replies
431
views
Trying to use equivalence test from a diffbind dataset
Diffbind R DESeq2 ChIP-seq ATAC-seq
updated 4 months ago by 85k • written 4 months ago by ▴ 20
0
votes
0
replies
262
views
Tutorial: DiffBind run parallel
CHIP-seq ATAC-seq DiffBind
updated 4 months ago by 85k • written 4 months ago by • 0
1
vote
1
reply
305
views
Diffbind fold values and parameter Fold in DBA.report function
DESEQ2 ATAC-seq DBA.report Diffbind
4 months ago by Manko47 ▴ 10
0
votes
4
replies
623
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
14 days ago by Ian 6.1k
0
votes
2
replies
400
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2 ATACseq DiffBind
5 months ago by atan • 0
1
vote
3
replies
538
views
DiffBind: no peaks in DBA
MACS2 DiffBind ChIP-seq
updated 6 months ago by ★ 18k • written 6 months ago by ▴ 10
0
votes
1
reply
317
views
Differential Accessibility
DiffBind
updated 6 months ago by 44k • written 6 months ago by • 0
0
votes
0
replies
670
views
Differential accessibility using DiffBinf
diffbind
6 months ago by Shloka • 0
0
votes
0
replies
293
views
Diffbind and DESeq2 comparison for differential sites
diffbind deseq2
updated 6 months ago by 44k • written 7 months ago by ▴ 500
1
vote
1
reply
502
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind r atacseq
7 months ago by Pierre Lindenbaum 164k
0
votes
3
replies
517
views
Why counting by diffbind and featurecounts differ?
featurecounts diffbind
updated 4 weeks ago by 6.1k • written 7 months ago by ▴ 500
0
votes
0
replies
220
views
Multifactor Analysis in DiffBind
DiffBind ChIPseq ChIP-seq
7 months ago by erbrocato • 0
4
votes
3
replies
543
views
Demonstrating lack of difference between two peaksets
DiffBind ChIP-seq
updated 7 months ago by 4.5k • written 7 months ago by ▴ 360
0
votes
2
replies
483
views
DiffBind issue in identification of differentially enriched peaks between two conditions
DiffBind ChIP-Seq
8 months ago by accibio ▴ 20
2
votes
1
reply
424
views
ATAC-seq downstream analysis
ATAC-seq diffbind
updated 8 months ago by 85k • written 8 months ago by ▴ 20
0
votes
0
replies
273
views
10X cellranger-atac generated bed files for DifBind
DiffBind 10x bed cellranger-atac
updated 8 months ago by 44k • written 8 months ago by • 0
0
votes
1
reply
307
views
Parameter bSubControl with no effect in dba.count?
DiffBind
updated 9 months ago by 44k • written 9 months ago by • 0
2
votes
3
replies
1.2k
views
DiffBind dba.normalize error using spikein reads
DiffBind ChIP-seq
updated 9 months ago by • 0 • written 2.7 years ago by ▴ 10
0
votes
2
replies
479
views
RStudio Diffbind analysis shows no result
galaxy diffbind rstudio
updated 9 months ago by 44k • written 9 months ago by ▴ 40
0
votes
2
replies
776
views
DiffBind; No sites have activity greater than filter value
diffbind
updated 9 months ago by 44k • written 14 months ago by • 0
2
votes
2
replies
830
views
DiffBind dba.contrast with design and/or categories parameters
ATAC DiffBind
updated 10 months ago by 146k • written 10 months ago by ▴ 30
2
votes
7
replies
1.2k
views
Multi-factor designs in DiffBind
Chipseq Multi-factor Diffbind
10 months ago by g.persic1991 ▴ 10
1
vote
3
replies
774
views
Consensus peaksets in DiffBind - conceptual questinos
DiffBind
updated 11 months ago by ★ 2.1k • written 11 months ago by ▴ 360
0
votes
1
reply
438
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind ChIP-seq
updated 11 months ago by ★ 2.1k • written 11 months ago by ▴ 20
3
votes
5
replies
1.2k
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run DiffBind ChIP-seq
updated 11 months ago by ★ 2.1k • written 11 months ago by ▴ 20
1
vote
2
replies
660
views
Diffbind low p-value but high FDR
ATAC-seq diffbind
11 months ago by LC ▴ 10
0
votes
4
replies
975
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
DiffBind csaw normalization spikein ChIPseq
11 months ago by jared.andrews07 ★ 18k
0
votes
0
replies
1.1k
views
Diffbind: can not load file Error in if ((length(callers) == 1) & (callers[1] == "counts")) { : argument is of length zero
Diffbind
11 months ago by makwana.kd ▴ 60
0
votes
0
replies
354
views
DiffBind:Using diffbind with only two replicates per condition
R ChipSeq DiffBind
12 months ago by shashankt693 • 0
2
votes
6
replies
2.6k
views
DiffBind reports no significant differentially enriched peaks
ChIP-seq DiffBind
updated 13 months ago by • 0 • written 2.0 years ago by ▴ 810
0
votes
0
replies
546
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq spike-in DiffBind
13 months ago by frueher • 0
1
vote
0
replies
370
views
Genes in open chromatin region
ATAC-seq DiffBind
13 months ago by Chris ▴ 340
0
votes
3
replies
796
views
DiffBind error: No contrasts added. There must be at least two sample groups with at least three replicates.
ATAC-seq DiffBind
updated 15 months ago by 44k • written 15 months ago by • 0
1
vote
2
replies
877
views
The bam file used for DiffBind?
DiffBind ATAC-seq
13 months ago by Miao Zhang • 0
2
votes
2
replies
721
views
How to compare peak profiles for a subset of ChIPseq genes
DiffBind composite-peak-profile ChIP-seq
15 months ago by bertb ▴ 20
3
votes
4
replies
8.6k
views
Help with DiffBind Generating report-based DBA object... Error: No valid contrasts/methods specified.
DiffBind
updated 15 months ago by ★ 18k • written 16 months ago by ▴ 340
1
vote
4
replies
1.1k
views
How to interpret chipseq profile plot
profileplyr profile-plot chipseq diffbind
updated 16 months ago by ★ 2.1k • written 16 months ago by ▴ 10
0
votes
1
reply
599
views
Profile Plot looks strange
profile-plot CHiP-Seq diffbind
updated 16 months ago by ★ 2.1k • written 16 months ago by ▴ 10
50 results • Page 1 of 1
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Clustering and dynamic tree cutting
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
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Recent Replies
Answer: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by wangziwei0010 ▴ 30
Hi ATpoint, Thank you for your though provoking answer. Big fans! Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs by Ming Tommy Tang ★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session by Dunois ★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra by Dunois ★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening by Ram 44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data by allingt • 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
Comment: Snakemake expand(): using a helper function (zip) and imputing wildcards? by Jesse ▴ 850
Not totally sure I'm right about your use case (are those config entries lists of strings, which is why you need to zip them?) but, you can…
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In general, you should threshold on the p value that corresponds to the maximum FDR you can accept. In practice, for scRNA-seq data, many g…
Comment: T cell subtype annotation by allingt • 0
I guess reference-based annotation is not an option? In my experience, visualising the expression of canonical markers (I don't know if CD4…
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