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8
votes
5
replies
1.3k
views
What is the difference between `possorted_genome_bam.bam` in the output of `cellranger count` and `sample_alignments.bam` in the output of `cellrange…
single-cell analysis RNA-seq velocity
updated 5 days ago by ★ 18k • written 19 months ago by ▴ 180
0
votes
1
reply
311
views
invalid class “DimReduc” object in `ArchR`
ArchR
updated 7 weeks ago by 5.8k • written 7 weeks ago by ▴ 180
0
votes
8
replies
5.8k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 7 months ago by • 0 • written 5.3 years ago by ▴ 180
6
votes
2
replies
679
views
How I should set `STAR` parameters to keep all the intronic reads?
STAR mapping
updated 8 months ago by ★ 6.9k • written 8 months ago by ▴ 180
6
votes
8
replies
1.5k
views
The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
RNA-velocity
updated 13 months ago by ▴ 70 • written 13 months ago by ▴ 180
0
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1
reply
1.5k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
13 months ago by Dan ▴ 180
1
vote
1
reply
1.5k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
13 months ago by Dan ▴ 180
1
vote
1
reply
1.5k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
13 months ago by Dan ▴ 180
8
votes
5
replies
1.2k
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome single-cell
updated 14 months ago by 85k • written 14 months ago by ▴ 180
0
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1
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1.2k
views
Comment: Comment: Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATA
14 months ago by Dan ▴ 180
3
votes
1
reply
643
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq ATAC-seq
updated 16 months ago by ★ 3.0k • written 16 months ago by ▴ 180
0
votes
0
replies
3.3k
views
Comment: Comment: umap failed to cluster the cells
16 months ago by Dan ▴ 180
6
votes
5
replies
3.3k
views
umap failed to cluster the cells
single-cell umap
16 months ago by Dan ▴ 180
1
vote
0
replies
414
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification ATAC
17 months ago by Dan ▴ 180
0
votes
0
replies
872
views
Comment: Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth?
17 months ago by Dan ▴ 180
2
votes
2
replies
872
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap deepTools
17 months ago by Dan ▴ 180
8
votes
9
replies
2.9k
views
Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st intron, ..., 3'UTR, intergenic, ...`
BAM
18 months ago by Dan ▴ 180
2
votes
0
replies
2.9k
views
Answer: Answer: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
18 months ago by Dan ▴ 180
0
votes
0
replies
627
views
Comment: Comment: `MOFAobject@expectations` is empty list
18 months ago by Dan ▴ 180
1
vote
2
replies
627
views
`MOFAobject@expectations` is empty list
MOFA2
updated 18 months ago by 44k • written 18 months ago by ▴ 180
0
votes
0
replies
909
views
Comment: Comment: What is difference between ` union.bed ` files and other `bed` files of `RSeQC`?
18 months ago by Dan ▴ 180
0
votes
0
replies
909
views
Comment: Comment: What is difference between ` union.bed ` files and other `bed` files of `RSeQC`?
18 months ago by Dan ▴ 180
4
votes
3
replies
909
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
18 months ago by Dan ▴ 180
0
votes
0
replies
548
views
How to save the digital percentage of `ChIPseeker::plotAnnoPie()` to a table?
ChIPseeker
19 months ago by Dan ▴ 180
0
votes
0
replies
2.9k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
19 months ago by Dan ▴ 180
0
votes
1
reply
2.9k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
19 months ago by Dan ▴ 180
0
votes
1
reply
2.9k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
19 months ago by Dan ▴ 180
1
vote
0
replies
2.9k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
19 months ago by Dan ▴ 180
0
votes
0
replies
172k
views
Comment: Comment: Extract Reads From A Bam File That Fall Within A Given Region
19 months ago by Dan ▴ 180
3
votes
0
replies
416
views
How to calculate the false discovery proportion from the p-value histogram?
false-discovery-rate
19 months ago by Dan ▴ 180
5
votes
1
reply
666
views
How to derive conditional maximum likelihood of the sum of independent negative binomial variables?
limma voom biostatistics
20 months ago by Dan ▴ 180
4
votes
0
replies
666
views
Answer: Answer: How to derive conditional maximum likelihood of the sum of independent negative
20 months ago by Dan ▴ 180
0
votes
0
replies
635
views
Comment: Comment: How to quantify the reads of each peak for ChIP-seq data?
21 months ago by Dan ▴ 180
3
votes
2
replies
635
views
How to quantify the reads of each peak for ChIP-seq data?
ChIP-seq DiffBind
21 months ago by Dan ▴ 180
3
votes
2
replies
679
views
How to find all of the new RNA splices from bulk RNA-seq data?
RNA-seq RNA-splices
updated 21 months ago by ★ 2.5k • written 21 months ago by ▴ 180
4
votes
2
replies
832
views
How to quantify the reads of peaks?
ChIP-seq ATAC-seq
updated 21 months ago by ▴ 20 • written 21 months ago by ▴ 180
0
votes
0
replies
963
views
Comment: Comment: Is there a package that can do downstream analysis of single-cell V(D)J sequenci
21 months ago by Dan ▴ 180
4
votes
3
replies
963
views
Is there a package that can do downstream analysis of single-cell V(D)J sequencing?
single-cell-VDJ
21 months ago by Dan ▴ 180
0
votes
1
reply
786
views
Comment: Comment: How to do Binding and Expression Target Analysis?
21 months ago by Dan ▴ 180
1
vote
3
replies
786
views
How to do Binding and Expression Target Analysis?
ChIP-seq
updated 21 months ago by 44k • written 21 months ago by ▴ 180
6
votes
4
replies
1.2k
views
How to install `BETA` on linux server?
ChIP-seq BETA
updated 21 months ago by 85k • written 21 months ago by ▴ 180
8
votes
7
replies
1.3k
views
6 follow
How should I deduce the variance and expectation of the logarithm of a variable in the `voom` paper?
Biostatistics voom limma
21 months ago by Dan ▴ 180
0
votes
2
replies
1.3k
views
Comment: Comment: How should I deduce the variable from its variance and expectation in the `voom`
21 months ago by Dan ▴ 180
2
votes
1
reply
614
views
How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`?
deepTools
updated 21 months ago by ★ 1.8k • written 21 months ago by ▴ 180
0
votes
0
replies
904
views
Comment: Comment: Is there a method to group and summarize the `homer` `findMotifsGenome.pl` outpu
21 months ago by Dan ▴ 180
2
votes
3
replies
904
views
Is there a method to group and summarize the `homer` `findMotifsGenome.pl` output?
Motif-analysis
21 months ago by Dan ▴ 180
0
votes
0
replies
468
views
How to customize the Profile values of `plotHeatmap` of `deeptools`?
deeptools
22 months ago by Dan ▴ 180
0
votes
1
reply
3.3k
views
Comment: Comment: umap failed to cluster the cells
23 months ago by Dan ▴ 180
2
votes
1
reply
1.1k
views
How can I customize `plotheatmap` of `deepTools` to different colors for different `.bed` file regions and how to customize the color of the intensit…
deepTools plotheatmap
updated 2.1 years ago by ▴ 100 • written 2.1 years ago by ▴ 180
0
votes
0
replies
839
views
Comment: Comment: Place to Acquire Bulk RNA-seq Cancer Datasets with Survival and Followup informa
2.2 years ago by Dan ▴ 180
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