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Questions tagged [figure-reproduction]

Use this tag if your question is about reproducing some figure or plot. Your figure should be using the same data or equivalent tools as the original plot.

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4 votes
1 answer
178 views

plotMA function issue: can not circle genes

I am trying to make MA-plot for my bulk-RNA-seq dataset and experiencing issues with it. I just copy-pasted the code that can be ...
Nikita Vlasenko's user avatar
3 votes
2 answers
744 views

How to transform and sort the matrix to make a heatmap showing signatures?

I have a matrix data with cells as rows and samples as columns. Here I am giving the data with dput ...
beginner's user avatar
  • 631
2 votes
1 answer
3k views

How I can reproduce this heat map

I have single cell RNA-seq on 8 time points. I have clustered each time point to 2-3 clusters by seurat. I also have a list of differentially expressed genes between all my 1562 cells in 8 time points....
Zizogolu's user avatar
  • 2,148
2 votes
0 answers
27 views

Method for reproducing minimal, cartoon-style protein structure visualisation

I recently came across a preprint ( DOI, PDF link ) that has some figures of protein structures in a style that I have not seen before. To me it appears easier on the eyes and less noisy than the ...
asimov's user avatar
  • 21
2 votes
0 answers
1k views

GO Term heatmap plot in terms of P value or fold enrichment

I'm clustering genes in terms of expression after clustering them. I'm taking out clusters and trying to find out what kind of GO terms are coming up. I came across this figure from this paper, I want ...
kcm's user avatar
  • 1,804
2 votes
0 answers
200 views

Reproducing population structure from 1000 Genomes Data

I recently tried to reproduce population structure with 1000 Genomes Project data (Phase 3, 2504 people). According to supplementary material, To reduce the dataset, we used VCFtools to only keep ...
In-Hee Lee's user avatar
2 votes
0 answers
449 views

Reproducing GTEx transcriptome analysis

I am willing to reproduce part of the analysis from "The human transcriptome across tissues and individuals" (Melé et all, 2015). I downloaded GTEx v6 FPKM data in txt format from GTEx portal. I want ...
carlesh's user avatar
  • 121
1 vote
1 answer
602 views

log2fold change as heatmap

From a paper: (D) Expression analysis of multiple lineage-specific differentiation markers in WT and PUS7-KO EBs (14 days). Heatmap shows log2 fold change (FC) PUS7-KO to WT for each individual ...
kcm's user avatar
  • 1,804
-2 votes
1 answer
128 views

Is it possible to get such a plot [closed]

I wish to reproduce a very informative plot in google Given a group of samples and a list of genes for which we have data how each genes has mutated and whether the alleles are homozygous of ...
Zizogolu's user avatar
  • 2,148