Moderator: geek_y
geek_y ♦ 11k
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- geek_y
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Experience in integrative analysis of over 30TB of various human genomics data sets like RNA/CAGE/ATAC/ChIP-Seq, “Hi-C” like and data from single-cell genomics using various data analysis techniques including exploratory data analysis (EDA), data visualization, statistics and machine learning. Comfortable with Python, R, shell scripting and HPC systems. Open to remote/freelancing opportunities.
https://gouthamatla.github.io/
Posts by geek_y
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Comment:
C: Integrate four scRNA-seq datas
... Thats not a QC, that's normalization.
> for (i in 1:length(pancreas.list)) {
>
> pancreas.list[[i]] <- **NormalizeData**(pancreas.list[[i]], verbose =
> FALSE)
>
> pancreas.list[[i]] <- FindVariableFeatures(pancreas.list[[i]],
> selection.method = "vst", nfeatures = 2 ...
written 7 weeks ago by
geek_y ♦ 11k
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... why not using a simple samtools, awk ? Like `samtools view in.sorted.bam | awk '{ if ($5<255) print }' | cut -f3,4` ...
written 7 weeks ago by
geek_y ♦ 11k
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... Thanks. Very intuitive. ...
written 7 weeks ago by
geek_y ♦ 11k
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... may be you can create sliding windows and count SNPs within them and keep the ones that has more than 'n' SNPs. and then merge overlapping windows post-hoc to have a consensus loci. This can be achieved by bedtools and a bit of scripting. I am not aware of any tools that does this. ...
written 8 weeks ago by
geek_y ♦ 11k
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... If you are merging two seurat objects by `merge` function from Seurat, the resulting object is a Seurat object. So you dont need to create one. I am not sure what you are trying to do. The link you attached is about data integration and here you are merging. ...
written 9 weeks ago by
geek_y ♦ 11k
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... What are these h1.rds and h2.rds ...
written 9 weeks ago by
geek_y ♦ 11k
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Comment:
C: CTCF motif orientation
... Have you tried anything ? Like searching in google ? ...
written 9 weeks ago by
geek_y ♦ 11k
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For bedtools intersect: keep pairing consistent
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For Multiple sequence alignment between multi fasta files ?
Scholar
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For A: Breaking down the reference genome chromosome-wise
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For A: Breaking down the reference genome chromosome-wise
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For A: Breaking down the reference genome chromosome-wise
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For A: Breaking down the reference genome chromosome-wise
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11 weeks ago,
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For Multiple sequence alignment between multi fasta files ?
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Popular Question
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created a question with more than 1,000 views.
For bedtools intersect: keep pairing consistent
Good Question
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For Convertion Of Gff3 To Gtf
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For A: Breaking down the reference genome chromosome-wise
Scholar
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For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Scholar
5 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Great Question
7 months ago,
created a question with more than 5,000 views.
For Multisample VCF file to Structure file format ?
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