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How to assess extent of cell-type admixtures from bulk RNA-seq data for a single tissue?

deconvolution scrna-seq cellmix rna-seq written 6 months ago by nancy • 60 • updated 6 months ago by YaGalbi • 1.4k

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Deconvolution Methods on RNA-Seq Data (Mixed cell types)

deconvolution rna-seq written 3.2 years ago by Paul.Lin • 90 • updated 13 months ago by inesdesantiago • 150

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deconvolution of heterogenous cell types in RRBS data

deconvolution methylome rrbs written 21 months ago by rahel14350 • 20

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RNA-Seq expression analysis of heterogeneous data (cancer+healthy cells)

deconvolution heterogeneous rna-seq written 23 months ago by Nicolas Rosewick ♦ 7.0k • updated 23 months ago by Steven Lakin • 1.4k

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Cellmix vs CellCODE

deconvolution written 2.6 years ago by chrisclarkson100 • 50 • updated 2.5 years ago by Biostar ♦♦ 20

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DNA sequence origin mapping [blast]

reads species deconvolution mapping written 3.1 years ago by Shicheng Guo • 7.3k

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blood deconvolution - cellmix

cellmix deconvolution microarray written 3.3 years ago by kuragari.ch • 20 • updated 3.2 years ago by Biostar ♦♦ 20

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Differential gene expession analysis in cell populations of mixed tumor and normal cells

deconvolution cell-type deseq rna-seq edger written 4.1 years ago by Christian • 2.7k

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Recent Replies

C: Amplicon Sequencing samples identification by gb • 520
If possible you should ask the lab. You can demultiplex with cutadapt or sabre... Mostly demultip...
C: FPKM quantile normalization by Maryam • 30
Yes, when I did not receive any reply from you, because I was in a hurry to do my project, I aske...
C: FPKM quantile normalization by Maryam • 30
Many thanks Kevin. I downloaded the genecode version 19 gtf file and put it in my document. I am ...
C: GATK 4 Mutect2 gives too much low depth variants by WouterDeCoster ♦ 35k
That's a common problem. When increasing the sensitivity, the probability of including false posi...
C: GATK 4 Mutect2 gives too much low depth variants by Zhizhong • 230
Yes, I would like to set minimal alt depth to 5, it is very hard to tell variants with very low f...
A: Concatenating metagenome samples by Carambakaracho • 620
Hi Jess and welcome at Biostars. To make it short: Yes your approach very likely will work. I d...
C: Subread and featurecounts read index and annotation once for all by bharata1803 • 390
Usually I use salmon, but this time the fastq is colorspace. So, I need to use aligner that suppo...
C: Subread and featurecounts read index and annotation once for all by WouterDeCoster ♦ 35k
Not what you are asking for, but if saving time is what you want (and you have a well-annotated o...
C: GATK 4 Mutect2 gives too much low depth variants by WouterDeCoster ♦ 35k
Well, isn't that what you would expect, that you find variants in a tumor with a low to very low ...
C: The fasta sequence does not match the REF allele at chr1:1298836 ? by finswimmer ♦ 8.0k
Hello https://www.biostars.org/u/50889/ , was the same `reference.fa`used for alignment? This d...
C: GATK DP filter for multiple samples by finswimmer ♦ 8.0k
`$ bcftools view -i 'FORMAT/DP>10' input.vcf > output.vcf` Or do I misunderstood something?...
C: Problem in using TCGAvisualize_meanMethylation function by 1303823432 • 0
Ok, thank you. I will try.

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