User: A248

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A24810
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Posts by A248

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How to use SingleR for annotating single-cell transcriptomics dataset with our own custom made bulk RNA data?
... Is this possible on the latest SingleR release version (3.10)? It looks like its fairly easy to use pre-existing Bulk RNA signatures from the built-in references, but when the bulk RNA data is generated by ourselves, is this possible? Thanks in advance! ...
annotation singler single cell sequencing written 8 months ago by A24810 • updated 8 months ago by jared.andrews076.9k
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Single cell cluster annotation and validation tools: recommendations?
... Hi, I am working on a single-cell dataset, would you have any recommendations for tools/algos for the following two aspects 1. After dimensionality reduction and cell clustering, we have annotated clusters based on general understanding of immunology (e.g. B cells annotated as such because they exp ...
sc-rna single cell sequencing rna-seq written 10 months ago by A24810 • updated 10 months ago by jared.andrews076.9k
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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 10 months ago by A24810 • updated 18 days ago by paria.alipour0
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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 11 months ago by A24810
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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 11 months ago by A24810 • updated 11 months ago by jared.andrews076.9k
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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 20 months ago by A24810
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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 2.4 years ago by A24810 • updated 2.4 years ago by genomax89k

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