User: egeulgen

gravatar for egeulgen
egeulgen670
Reputation:
670
Status:
Trusted
Location:
Istanbul
Website:
https://github.com/ege...
Scholar ID:
Google Scholar Page
Last seen:
3 days, 15 hours ago
Joined:
2 years, 5 months ago
Email:
e*******@gmail.com

Posts by egeulgen

<prev • 25 results • page 1 of 3 • next >
1
vote
0
answers
75
views
0
answers
BWA - [fread] Input/output error
... Hello all, I'm trying to align paired-end read files to the reference genome using the following command (bwa version: 0.7.17-r1188): `bwa mem $ref_genome_fasta Sample_R1_001.fastq.gz Sample_R2_001.fastq.gz` I get the following error after a few seconds: `[fread] Input/output error` [UPDATE] I ...
software error alignment bwa written 11 days ago by egeulgen670
1
vote
0
answers
2.5k
views
0
answers
Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... thank you. glad you like the tutorial. Performing the analysis with p-values would be wrong, I would suggest instead to change the p value threshold (i.e. to change the argument `p_val_threshold `) to a higher value (e.g. 0.1). ...
written 3 months ago by egeulgen670
0
votes
0
answers
2.5k
views
0
answers
Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... In some cases (especially if the number of input genes is low), pathfindR may not find any active subnetworks and therefore no enriched pathways. The message stating "Could not find any interactions for XX (XX%) genes in the PIN." is more relevant for genes not mapping onto the PIN. ...
written 4 months ago by egeulgen670
0
votes
0
answers
2.5k
views
0
answers
Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Yes you should use your own expression data. **This is the data you used to perform differential expression analysis** and obtain the logFC and p values. pathfindR does not (cannot) create the expression data as it only uses the logFC values provided for enrichment. The expression matrix (input of l ...
written 4 months ago by egeulgen670
0
votes
0
answers
2.5k
views
0
answers
Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hey, The expression matrix is the matrix you used to perform the differential expression test. Something like: GSM389703 GSM389704 GSM389705 FAM110A 9.8591 10.529 11.3828 RNASE2 10.3410 10.400 9.1157 S100A8 14.9554 15.012 12.9907 For the example da ...
written 4 months ago by egeulgen670
0
votes
1
answer
517
views
1
answers
Comment: C: Allele frequency comparison by Fisher's exact test
... I provided the example R code in my response (see above). There N_SNP is replaced with 3000 and for fisher.test you have to do something like: fisher.test(table(my_genotypes[i, ], 1kg_genotypes[i, ])) This does depend on how you store the two. ...
written 4 months ago by egeulgen670
1
vote
1
answer
517
views
1
answers
Answer: A: Allele frequency comparison by Fisher's exact test
... You may perform multiple Fisher's exact test, store the p values and then adjust them. In R, you would do something along the lines of: ### Perform Fisher's exact and store the p-values p_vals <- c() for (i in 1:N_SNPS) { result <- fisher.test(...) p_vals <- c( ...
written 4 months ago by egeulgen670
0
votes
0
answers
1.4k
views
0
answers
Comment: C: pathfindR - Pathway Enrichment Analysis using Active Subnetworks
... The expression matrix for the pathway scores is the same matrix as the one you use for differential expression analysis. Columns are samples, rows are genes and the values are expression values. ...
written 7 months ago by egeulgen670
0
votes
2
answers
642
views
2
answers
Comment: C: Plotting the expression values for two genes in a range of cells
... you have to have a column called `Cell` filled with the row names, i.e. `"cell1, cell2, ..."` should be in a column named `Cell` ...
written 9 months ago by egeulgen670
5
votes
2
answers
642
views
2
answers
Answer: A: Plotting the expression values for two genes in a range of cells
... You can plot such a "lollipop plot" using ggplot2: cell_data <- read.csv("~/Downloads/data.csv") library(reshape2) library(ggplot2) cell_data_molten <- melt(cell_data) cell_data$Total <- cell_data$Gene.A + cell_data$Gene.B for_levels <- cell_data$C ...
written 9 months ago by egeulgen670

Latest awards to egeulgen

Popular Question 3 months ago, created a question with more than 1,000 views. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Popular Question 5 months ago, created a question with more than 1,000 views. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Librarian 5 months ago, created a post with more than 10 bookmarks. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Prophet 8 months ago, created a post with more than 20 followers. For Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
Appreciated 9 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR
Scholar 9 months ago, created an answer that has been accepted. For A: Plotting the expression values for two genes in a range of cells
Appreciated 9 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Appreciated 10 months ago, created a post with more than 5 votes. For pathfindR - Pathway Enrichment Analysis using Active Subnetworks
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: enrichment of gene set with enrichR
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: enrichment of gene set with enrichR

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1779 users visited in the last hour