User: A248

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A2480
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Posts by A248

<prev • 5 results • page 1 of 1 • next >
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Best package to cluster a single cell dataset using marker gene lists retrieved from elsewhere?
... Say for example we have a PBMC single cell dataset generated in the lab, and would wish to use differentially expressed gene lists of different cell types (B, T, monocyte etc) which have been published elsewhere to guide the clustering of our single cell dataset. Is there a package which would be ...
single cell sequencing rna-seq clustering written 1 day ago by A2480 • updated 1 day ago by jared.andrews073.9k
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Comment: C: Algorithm for clustering single cells based on SNPs?
... thanks! we don't have a VCF file for this particular species we are working with, which would be problem with vartrix. We are only planning to focus on the genes which are highly expressed across >90% of cells (mitochondrial genes in particular), as we are not interested in identifying genome w ...
written 25 days ago by A2480
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Algorithm for clustering single cells based on SNPs?
... We have single cell data which was pooled from 3 different organisms (same species) into one sample (processed using CellRanger and Seurat 3). We are now trying to de-segregate the cells based on organism by using SNP variation. What would be the best algorithm for this? Thanks! ...
forum single cell snp 10x genomics written 26 days ago by A2480 • updated 26 days ago by jared.andrews073.9k
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How can I retrieve TPM values for selected genes from transcriptome data in a Bioproject on NCBI?
... https://www.ncbi.nlm.nih.gov/bioproject?LinkName=biosample_bioproject&from_uid=4262220 The Bioproject I am interested in is the above, containing transcriptome data from different tissues in Rousettus aegypticus. There are 21 biosamples in this collection (each containing data from a different ...
genome assembly next-gen rna-seq written 10 months ago by A2480
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How can I download a fasta file of all homologs to a given protein?
... I have the amino acid sequence of a gene of interest. I want to identify all the different homologs in different species, and assemble it in a single FASTA file format. Which I then want to input into a sequence similarity network (SSN) tool, to find how the different homologs from different species ...
alignment sequence written 19 months ago by A2480 • updated 19 months ago by genomax74k

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