User: bioinformatics.cancer

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Posts by bioinformatics.cancer

<prev • 32 results • page 1 of 4 • next >
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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 4 months ago by bioinformatics.cancer170 • updated 9 weeks ago by dppb0560
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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 8 months ago by bioinformatics.cancer170
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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 14 months ago by bioinformatics.cancer170
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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 14 months ago by bioinformatics.cancer170 • updated 5 months ago by Friederike2.0k
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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 16 months ago by bioinformatics.cancer170 • updated 16 months ago by Jean-Karim Heriche16k
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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 21 months ago by bioinformatics.cancer170 • updated 20 months ago by ATpoint6.5k
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Adaptive T cell receptor productive clone missing
... Hi, I am analyzing T Cell Receptor sequencing data received from Adaptive Biotechnology which consists of summarized clonotype data which includes NT and AA sequence among many other variables. Some of the clones don't have an AA sequence but have a NT sequence. I believe these are called "unproduc ...
adaptive productive clone tcr sequencing written 21 months ago by bioinformatics.cancer170 • updated 21 months ago by mikhail.shugay3.3k
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TCR RNAseq Single Cell Data Analysis
... Hi, I have an RNAseq data from TCR alpha and bed chain single cell sequencing which I am trying to analyze. I looked at the post https://www.biostars.org/p/148371/ and also read the Mark Davis paper and the protocol, which I thought would be appropriate to follow. But I cannot either find the dat ...
immunoseq paired tcr single cell rna-seq written 21 months ago by bioinformatics.cancer170 • updated 13 months ago by carina.dehner0
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Comment: C: TCR sequence analysis
... Hi Bin, I am a bioinformatician in the cancer immunotherapy lab at Duke university and have just started working on a single cell TCR sequencing project. I was also trying to follow the Mark Davis paper that you referenced. It seems they had modified vdjfasta for TCR but I am not sure if the modif ...
written 22 months ago by bioinformatics.cancer170

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