User: mmalumbresm

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Posts by mmalumbresm

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Best correlation between the expression of a given gene and the rest of genes in scRNAseq data
... I am analyzing single cell RNA seq data with scanpy and I would like to find a method to find which gene(s) display the best correlation in their expression profile when compared to a gene of my choice. Any suggestion? Python-based would be great but any suggestion welcome! Thanks for your help! ...
gene expression correlation rna-seq written 2 days ago by mmalumbresm0
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Comment: C: GSEA Positional Gene sets for mouse chromosomes
... Wooww! That's a fantastic resource. Many thanks for the link! ...
written 2 days ago by mmalumbresm0
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GSEA Positional Gene sets for mouse chromosomes
... I am trying to analyze enrichment of gene expression (preranked GSEA) based on the position of each gene in the mouse genome. I found a gene set (gmt) file that contains the list of genes for each human chromosome and each cytogenetic band (GSEA/MSigDB; https://www.gsea-msigdb.org/gsea/msigdb/collec ...
geneset mouse chromosome cytogenetic band gsea written 7 days ago by mmalumbresm0 • updated 7 days ago by Gordon Smyth1.7k
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Comment: C: split BAM file with same cell-barcode and UMI pair
... Did you find a solution for this? I have also generated R2.fastq files tagged with the cell-barcode and UMI (using UMI tools) and mapped the reads (with STAR). The resulting bam files contain the cell barcode in the alignments and I would like to split the alignments for the different cells to perfo ...
written 11 days ago by mmalumbresm0

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