User: bioinformatics.cancer

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Posts by bioinformatics.cancer

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Comment: C: Data integration strategies for single cell RNA-seq
... Thanks for the suggestion. Yes, I have looked into the vignette but I don't believe that one is similar to the situation I described. For the alignment vignette, the starting condition is the same except that the stimulation is expected to give difference in gene expression rather than yield very ...
written 4 months ago by bioinformatics.cancer180
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Data integration strategies for single cell RNA-seq
... Hi, I was writing to see if anyone has experience combining single cell RNA-seq data from different conditions and biological/technical replicates in an experiment. I have a dataset with two different conditions (WT/Treatment) and each condition has two different replicates (done in different isoge ...
scrnaseq data integration rna-seq written 4 months ago by bioinformatics.cancer180 • updated 4 months ago by genomax69k
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Single Cell RNAseq Imputation in Seurat
... Hi, I was writing to find out if anyone has experience doing imputation in Seurat. Where in the workflow steps would you suggest to use the function “addImputedScore” and once this is done will the imputed values be picked up by the Clustering function (FindCluster) to make use of the imputed valu ...
imputation rna-seq single cell written 10 months ago by bioinformatics.cancer180 • updated 8 months ago by kristoffer.vittingseerup2.0k
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Single cell RNA sequencing Seurat and Monocle
... Hi, I am analyzing some single cell rna-seq data sets with Seurat and would like the follow up the analysis with cell trajectory analysis using monocle. In order to keep the analysis in sync I would like to use the pre-processed expression matrix in monocle (i.e., the normalized, scaled, transform ...
seurat cell trajectory rna-seq single cell monocle written 15 months ago by bioinformatics.cancer180 • updated 13 months ago by dppb0570
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Takara Mouse TCR a/b Profiling Sample Multiplexing
... Hi, We would like to use the Takara Bio SMARTer Mouse TCR a/b Profiling kit for mouse TCR sequencing and are trying to figure out how many samples can be multiplexed using Illumina indexes on a single MiSeq v3 sequencer lane (PE 2x300 bp reads) to determine the cost of sequencing. Our sequencing co ...
takara tcr rna-seq written 19 months ago by bioinformatics.cancer180
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Imaging mass cytometry data analysis
... Hi, We have an imaging mass cytometry data set that we need to analyze. I have done some Flow Cytometry and Mass Cytometry data analysis but not "imaging" cytometry data. In searching I have not found any tools specific for this type of data set. Thanks, - Pankaj ...
mass cytometry data analysis written 2.1 years ago by bioinformatics.cancer180
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Single Cell RNA-seq Mitochondrial Gene Expression
... Hi, I am analyzing a Single Cell RNA-seq data set and most of the top highly variables genes are mitochondrial genes. These are not genes of interest and I am primarily interested in nuclear genes. Is it ok to remove the mitochondrial genes from the gene expression matrix before analysis? Also cu ...
mitochondrial expression rna-seq single cell written 2.1 years ago by bioinformatics.cancer180 • updated 16 months ago by Friederike4.5k
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KEGG Cancer Pathway
... Hi, I have used KEGG for pathway analysis for a gene expression data set and one of the pathways that comes up enriched is the "Pathways in Cancer" (hsa05200). This is a very generic pathway with many components. The diagram shows several processes within the pathway such as "Metastasis", "Evading ...
pathway kegg cancer written 2.2 years ago by bioinformatics.cancer180 • updated 2.2 years ago by Jean-Karim Heriche20k
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rna-seq expression analysis using normalized TPM
... Hi, I have a gene expression data set from RNA-seq that had gene level normalized TPM counts. From what I have been able to find it appears that the tool best suited for this type of data is EBSeq. The vignette says that the expression counts should not be normalized. I was if I could use EBSeq a ...
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MCF-7 Cell Line DNA Sequence Data
... Hi, We are planning to analyze some cancer cell lines for variants such as mutations, gene fusions and structural variants. I am looking for sequencing data for MCF-7 cell line. I have been able to find RNA-seq sequencing data from CCLE but cannot find DNA sequencing data. Does anyone know if MCF ...
wxs wgs cancer cell line dna sequence mcf-7 written 2.7 years ago by bioinformatics.cancer180 • updated 2.6 years ago by ATpoint19k

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