User: aloke205

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aloke20530
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Posts by aloke205

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Comment: C: Clustering for Single-cell RNA-seq Data
... Thanks @mkgupta.bioinfo for the information :) I will try to generate matrix and heatmap as suggested by you. ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... Thanks for your reply. Yes, now I am understanding what I am doing and I am really grateful to you because this was not possible without your guidance. I have one more question :) Could you please tell if I have estimated fractions for each cluster in a correct way in the above example. Though I ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... Hii Friederike, I tried to make fractions for each cluster. written below is the sample result cl_ID cs_ID cs_count cs_total_count (cs_count/cs_total_count) 1 5 1 9 0.1111111 1 26 1 8 0.125 2 1 1 ...
written 3 months ago by aloke20530 • updated 3 months ago by RamRS24k
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Comment: C: Clustering for Single-cell RNA-seq Data
... Hii Friederike, I have been able to count how many times each cluster ID is present within each CloneID group e.g. cloneID ClusterID count 1 5 1 1 26 1 2 1 1 2 2 2 ...
written 3 months ago by aloke20530 • updated 3 months ago by genomax74k
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Comment: C: Clustering for Single-cell RNA-seq Data
... Two different cells with same clone ID means these different two cells share the same lineage ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... Thank you for answering in detail. Yes, in our analysis "clonally related" means "cells that have the same Clone ID". After reading your answer, I cross-examined my data-set and find out that there are numerous group of cells that share the same clone ID. I will try to solve the problem as sugge ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... Thanks a lot for your answer. This is very useful for me. My main problem is with understanding how to quantify if cells within or across clusters are clonally related using the above csv file. Additionally, I am new to this type of analysis and my professor asked me to quantify the result in on ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... Yes.. I am looking for the same. Could you please help me? ...
written 3 months ago by aloke20530
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Comment: C: Clustering for Single-cell RNA-seq Data
... I have been able to generate heatmap (available at the link below) using ComplexHeatmap as guided by @RamRS As I am new to this analysis, I am stuck how to detect if cells within or across clusters are clonally related. Hence asking for help :( ...
written 3 months ago by aloke20530
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Clustering for Single-cell RNA-seq Data
... Dear members, I have a csv file from Single-cell RNA-seq experiment with three column: unique Cell-IDs (First column), Cluster-IDs (Second column) and CloneIDs (Third) I need to generate heat-map using this csv file in R to detect if cells within or across clusters are clonally related. Please ...
single-cell R clustering written 3 months ago by aloke20530

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