User: rprog008

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rprog00830
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Posts by rprog008

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Distance matrix for monocle and seurat object
... I apologize, if my question is unclear. I am trying to retrieve the distance matrix from both seurat and monocle object in matrix form. For instance in case of monocle, if I am writing cellPairwiseDistances(HSMM) or HSMm@cellPairwiseDistances I am getting 0x0 matrix. However, clu ...
written 15 days ago by rprog00830
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Distance matrix for monocle and seurat object
... Dear members, I am trying to create a distance matrix for both Seurat and monocle object for clustering analysis of single cell RNA data analysis. Though I am following the tutorial in their respective websites, i am unable to retrieve distance matrix in any way. Below is code ...
single cell rna monocle seurat written 15 days ago by rprog00830
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Comment: C: create a double bar plot to compare data
... Though I am not an expert. but I think this link may solve your problem http://www.sthda.com/english/wiki/ggplot2-barplots-quick-start-guide-r-software-and-data-visualization ...
written 21 days ago by rprog00830
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Comment: C: Need help with codeml
... Thanks Brice for the answer. I am facing one more problem. What if p-value of LRT between M1a vs M2a is unsignificant while p-value of LRT between M0-M3, M7 vs M8 and M8 vs M8a is significant. I am sorry if this seems naive question. Please suggests me ...
written 24 days ago by rprog00830
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Comment: C: Need help with codeml
... Thanks a lot for clearing my doubt and for sharing interesting articles. :) ...
written 25 days ago by rprog00830
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Need help with codeml
... Dear member, I am performing analysis with various models of codeml to detect pattern on evolution on a disease gene set. I am performing the same analysis on 6 and 16 species of mammal, separately. Though in both the cases I am getting my gene sets are evolving under purifying ...
purifying selection codeml written 26 days ago by rprog00830 • updated 25 days ago by Brice Sarver3.2k
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Comment: C: is lineage analysis same as trajectory analysis
... Thanks @ignor.. i will have a look at it.. i am trying to detect pattern how two cell types originate from a same progenitor cell. Note: Its seems this works more or less like monocle. Thus I am still in doubt. :( ...
written 5 weeks ago by rprog00830
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is lineage analysis same as trajectory analysis
... Dear member, I am trying to perform lineage analysis with single cell RNA sequencing data. recently I have came across trajectory analysis with monocle. As I am naive in this field, I am bit confused if this trajectory analysis will give me same result of lineage analysis. I would ...
lineage analysis trajectory analysis written 5 weeks ago by rprog00830
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Estimate lineage coupling score through R
... Dear member, I am trying to estimate lineage coupling score through R from a table containing three columns as given below ``` Uniqure Cell-IDs Cluster-IDS cloneID XX1_A06 3 1 XX1_B01 1 5 XC2_C03 3 8 XX2_C04 2 1 XX3_C05 3 9 ``` I need to calculate a z-score to find out which clusters are couple ...
lineage coupling score written 8 weeks ago by rprog00830
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Comment: C: Number of species for positive selection analysis
... read again my first comment... 😑☺ i said less than 10 may be questionable sometime.. i never said always. others too are claiming going for 10 sequence is a rule of thumb. one of the reason already stated by aloke and others. my intention was to state why not to play safe rather than repeating you ...
written 7 months ago by rprog00830

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