Moderator: geek_y

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geek_y11k
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Barcelona
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geek_y
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8 years, 6 months ago
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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

<prev • 1,550 results • page 1 of 155 • next >
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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_y11k
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Comment: C: RNA-seq STAR genome mapping
... Good catch. ...
written 7 weeks ago by geek_y11k
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Comment: C: How to find all mapped locations of a read from PySam?
... 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_y11k
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Comment: C: filtered tab delimited file with awk
... amazing, as usual. ...
written 7 weeks ago by geek_y11k
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Comment: C: differential gene expression analysis
... Thanks. Very intuitive. ...
written 7 weeks ago by geek_y11k
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Comment: C: differential gene expression analysis
... What is GSE ? ...
written 8 weeks ago by geek_y11k
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Comment: C: Keeping loci those have specific number of SNPS
... 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_y11k
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Comment: C: merge two SeuratObjects to do the integration
... 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_y11k
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Comment: C: merge two SeuratObjects to do the integration
... What are these h1.rds and h2.rds ...
written 9 weeks ago by geek_y11k
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Comment: C: CTCF motif orientation
... Have you tried anything ? Like searching in google ? ...
written 9 weeks ago by geek_y11k

Latest awards to geek_y

Popular Question 4 weeks ago, created a question with more than 1,000 views. For bedtools intersect: keep pairing consistent
Great Question 4 weeks ago, created a question with more than 5,000 views. For Multiple sequence alignment between multi fasta files ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Great Question 11 weeks ago, created a question with more than 5,000 views. For Multiple sequence alignment between multi fasta files ?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 3 months ago, created a question with more than 1,000 views. For bedtools intersect: keep pairing consistent
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For Convertion Of Gff3 To Gtf
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 4 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
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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