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compgenomr/book
Error in validObject(.Object) : invalid class "ScoreMatrix" object: superclass "mMatrix" not defined in the environment of the object's class

Hello The code of line 530-558 in the 06-genomicIntervals.Rmd can t run successfully: # get transcription start sites on chr20 library(genomation) transcriptFile=system.file( extdata , ...
  • danli349
  • 1
  • Opened 
    on Feb 22, 2024
  • #71

compgenomr/book
problems on R 4.1.0 on a DELL laptop

Text was cut and pasted from electronic version of book at https://compgenomr.github.io/book/ A small amount of follow up carried out see if there was a simple explanation or work around but no attempt ...
  • al2na
  • Opened 
    on Oct 5, 2021
  • #64

compgenomr/book
edit stats exercise question for clarity

Stats chapter: How does the estimate from the random samples change if we simulate more data with data=matrix(rnorm(6000,mean=200,sd=70),ncol=6) should be How does the estimate from the random samples ...
  • al2na
  • Opened 
    on Aug 17, 2021
  • #63

compgenomr/book
used d() instead of fread(), change this to fread()

https://github.com/compgenomr/book/blob/08d3028754f68cd1fc16bc80318cf53af0ac7946/02-intro2R.Rmd#L359
  • al2na
  • Opened 
    on Jun 23, 2021
  • #62

compgenomr/book
Figure 11.9 is mis-attributed

FIGURE 11.9: A heatmap of NMF factors shows the separability of tumors into subtype clusters. This plot is more useful than a scatter plot when there are more than two factors. This figure is misattributed ...
  • ankushs0128
  • Opened 
    on Mar 2, 2021
  • #58

compgenomr/book
expression data section 4.1.1

I cannot find the code used to create df (table for expression data of leukemia patients) in clustering section 4.1.1.
  • fazeln
  • 3
  • Opened 
    on Nov 25, 2020
  • #55

compgenomr/book
Typo in section 2.6.1.

Hello, There is a typo in section 2.6.1: library(data.table) df.f=d(enhancerFilePath, header = FALSE,data.table=FALSE) It shoud say: library(data.table) df.f=fread(enhancerFilePath, header = FALSE,data.table=FALSE) ...
  • coforfe
  • Opened 
    on Nov 22, 2020
  • #54

compgenomr/book
Missing license in repository root

While the license is clearly indicated on the landing page of the book it is missing in the repository root. Please consider adding the license.
  • fabianegli
  • Opened 
    on Oct 25, 2020
  • #52

compgenomr/book
Unable to Open in PDF Format

Hello! I m unable to open this in a PDF format, and instead have to access the book through the web interface. This is fine, but there is a PDF link/icon at the top right of the text, and it takes you ...
  • bentoske
  • 3
  • Opened 
    on Sep 20, 2020
  • #51

compgenomr/book
Typos on chapter 3

Hi, I just want to report typos you may have missed: Chapter 3 3.1.2 Describing the spread: measurements of variation: In the probability section : You have written : In this case, what we want is the ...
  • nezlicodes
  • Opened 
    on Jul 4, 2020
  • #43
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