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10
votes
5
replies
2.7k
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…
velocity RNA-seq single-cell
updated 10 months ago by 45k • written 2.5 years ago by ▴ 180
0
votes
1
reply
781
views
invalid class “DimReduc” object in `ArchR`
ArchR
updated 11 months ago by 6.5k • written 11 months ago by ▴ 180
0
votes
8
replies
6.6k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 17 months ago by • 0 • written 6.1 years ago by ▴ 180
6
votes
2
replies
1.3k
views
How I should set `STAR` parameters to keep all the intronic reads?
STAR mapping
updated 19 months ago by ★ 7.7k • written 19 months ago by ▴ 180
6
votes
8
replies
2.6k
views
The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
RNA-velocity
updated 24 months ago by ▴ 80 • written 24 months ago by ▴ 180
0
votes
1
reply
2.6k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
24 months ago by Dan ▴ 180
1
vote
1
reply
2.6k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
24 months ago by Dan ▴ 180
1
vote
1
reply
2.6k
views
Comment: Comment: The RNA velocity are opposite in 'dynamical' and 'stochastic' modes.
24 months ago by Dan ▴ 180
8
votes
5
replies
1.9k
views
Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATAC data analysis?
multiome single-cell
updated 2.0 years ago by 89k • written 2.0 years ago by ▴ 180
0
votes
1
reply
1.9k
views
Comment: Comment: Is there a benchmark analysis for the best tool for multiome single-cell RNA+ATA
2.0 years ago by Dan ▴ 180
3
votes
1
reply
973
views
Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?
ChIP-seq ATAC-seq
updated 2.2 years ago by ★ 3.1k • written 2.2 years ago by ▴ 180
0
votes
0
replies
4.8k
views
Comment: Comment: umap failed to cluster the cells
2.2 years ago by Dan ▴ 180
6
votes
5
replies
4.8k
views
umap failed to cluster the cells
single-cell umap
2.2 years ago by Dan ▴ 180
1
vote
0
replies
619
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification ATAC
2.3 years ago by Dan ▴ 180
0
votes
0
replies
1.5k
views
Comment: Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth?
2.3 years ago by Dan ▴ 180
2
votes
2
replies
1.5k
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap deepTools
2.3 years ago by Dan ▴ 180
8
votes
9
replies
3.8k
views
Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st intron, ..., 3'UTR, intergenic, ...`
BAM
2.4 years ago by Dan ▴ 180
2
votes
0
replies
3.8k
views
Answer: Answer: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
2.4 years ago by Dan ▴ 180
0
votes
0
replies
966
views
Comment: Comment: `MOFAobject@expectations` is empty list
2.4 years ago by Dan ▴ 180
1
vote
2
replies
966
views
`MOFAobject@expectations` is empty list
MOFA2
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 180
0
votes
0
replies
1.3k
views
Comment: Comment: What is difference between ` union.bed ` files and other `bed` files of `RSeQC`?
2.4 years ago by Dan ▴ 180
0
votes
0
replies
1.3k
views
Comment: Comment: What is difference between ` union.bed ` files and other `bed` files of `RSeQC`?
2.4 years ago by Dan ▴ 180
4
votes
3
replies
1.3k
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
2.4 years ago by Dan ▴ 180
0
votes
0
replies
794
views
How to save the digital percentage of `ChIPseeker::plotAnnoPie()` to a table?
ChIPseeker
2.4 years ago by Dan ▴ 180
0
votes
0
replies
3.8k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
2.4 years ago by Dan ▴ 180
0
votes
1
reply
3.8k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
2.4 years ago by Dan ▴ 180
0
votes
1
reply
3.8k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
2.4 years ago by Dan ▴ 180
1
vote
0
replies
3.8k
views
Comment: Comment: Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st
2.4 years ago by Dan ▴ 180
0
votes
0
replies
191k
views
Comment: Comment: Extract Reads From A Bam File That Fall Within A Given Region
2.4 years ago by Dan ▴ 180
3
votes
0
replies
748
views
How to calculate the false discovery proportion from the p-value histogram?
false-discovery-rate
2.4 years ago by Dan ▴ 180
5
votes
1
reply
990
views
How to derive conditional maximum likelihood of the sum of independent negative binomial variables?
limma voom biostatistics
2.5 years ago by Dan ▴ 180
4
votes
0
replies
990
views
Answer: Answer: How to derive conditional maximum likelihood of the sum of independent negative
2.5 years ago by Dan ▴ 180
0
votes
0
replies
946
views
Comment: Comment: How to quantify the reads of each peak for ChIP-seq data?
2.6 years ago by Dan ▴ 180
3
votes
2
replies
946
views
How to quantify the reads of each peak for ChIP-seq data?
ChIP-seq DiffBind
2.6 years ago by Dan ▴ 180
3
votes
2
replies
1.0k
views
How to find all of the new RNA splices from bulk RNA-seq data?
RNA-seq RNA-splices
updated 2.6 years ago by ★ 3.1k • written 2.6 years ago by ▴ 180
4
votes
2
replies
1.2k
views
How to quantify the reads of peaks?
ChIP-seq ATAC-seq
updated 2.6 years ago by ▴ 20 • written 2.6 years ago by ▴ 180
0
votes
0
replies
1.4k
views
Comment: Comment: Is there a package that can do downstream analysis of single-cell V(D)J sequenci
2.6 years ago by Dan ▴ 180
4
votes
3
replies
1.4k
views
Is there a package that can do downstream analysis of single-cell V(D)J sequencing?
single-cell-VDJ
2.6 years ago by Dan ▴ 180
0
votes
1
reply
1.1k
views
Comment: Comment: How to do Binding and Expression Target Analysis?
2.6 years ago by Dan ▴ 180
1
vote
3
replies
1.1k
views
How to do Binding and Expression Target Analysis?
ChIP-seq
updated 2.6 years ago by 45k • written 2.6 years ago by ▴ 180
6
votes
4
replies
1.7k
views
How to install `BETA` on linux server?
ChIP-seq BETA
updated 2.6 years ago by 89k • written 2.6 years ago by ▴ 180
8
votes
7
replies
1.9k
views
6 follow
How should I deduce the variance and expectation of the logarithm of a variable in the `voom` paper?
Biostatistics voom limma
2.6 years ago by Dan ▴ 180
0
votes
2
replies
1.9k
views
Comment: Comment: How should I deduce the variable from its variance and expectation in the `voom`
2.6 years ago by Dan ▴ 180
2
votes
1
reply
899
views
How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`?
deepTools
updated 2.6 years ago by ★ 1.9k • written 2.6 years ago by ▴ 180
0
votes
0
replies
1.3k
views
Comment: Comment: Is there a method to group and summarize the `homer` `findMotifsGenome.pl` outpu
2.6 years ago by Dan ▴ 180
2
votes
3
replies
1.3k
views
Is there a method to group and summarize the `homer` `findMotifsGenome.pl` output?
Motif-analysis
2.6 years ago by Dan ▴ 180
0
votes
0
replies
657
views
How to customize the Profile values of `plotHeatmap` of `deeptools`?
deeptools
2.7 years ago by Dan ▴ 180
0
votes
1
reply
4.8k
views
Comment: Comment: umap failed to cluster the cells
2.7 years ago by Dan ▴ 180
2
votes
1
reply
1.5k
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 2.9 years ago by ▴ 100 • written 3.0 years ago by ▴ 180
0
votes
0
replies
1.2k
views
Comment: Comment: Place to Acquire Bulk RNA-seq Cancer Datasets with Survival and Followup informa
3.0 years ago by Dan ▴ 180
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