User: Gian

gravatar for Gian
Gian350
Reputation:
350
Status:
Trusted
Location:
Canada
Last seen:
9 months, 1 week ago
Joined:
5 years ago
Email:
n*******@gmail.com

Posts by Gian

<prev • 34 results • page 1 of 4 • next >
0
votes
1
answer
1.2k
views
1
answers
Answer: A: How to identify transcription factors (TFs) from expression data comparison?
... Are these human cell lines? If you are interested in identifying TFs that might regulate a differentially expressed gene you can calculate the correlation between the expression profile of your gene and a list of TFs. Considering that the expression profile only includes 10 samples you probably woul ...
written 3.6 years ago by Gian350
1
vote
1
answer
906
views
1
answers
Answer: A: GEO - Cannot find processed gene expression data ?
... You can find the gene RPKM values for the different samples in GSE56227_RAW.tar in the download section. Sometimes the processed gene expression is in the Series Matrix File but usually for array data.   ...
written 3.6 years ago by Gian350
1
vote
0
answers
1.3k
views
0
answers
Comment: C: How to perform correlation between unmatched miRNA and mRNA data?
... First you need to exclude the samples that are not in both datasets and then you can calculate the correlation on the overlapping subset. Since you are using R you can merge the two matrix and then calculate Spearman correlation between all miRNAs and mRNA       ...
written 3.6 years ago by Gian350
0
votes
0
answers
1.3k
views
0
answers
Comment: C: How to perform correlation between unmatched miRNA and mRNA data?
... I think you should explain what you mean with 'unmatched', you can only calculate correlation on matching samples. ...
written 3.6 years ago by Gian350
0
votes
1
answer
1.4k
views
1
answers
Answer: A: Probing specific protein amino acid position changes in R
... There are indeed many different function that you can use to manipulate strings, this is an example using Biostrings: #load package library(Biostrings) #reference sequence standardseq<- AAString("MARKSLEMSIR") #query sequences seq1 <- AAString("MARKSLEMSER") seq2 <- AAString("MDRKSLEMS ...
written 3.6 years ago by Gian350
1
vote
2
answers
1.9k
views
2
answers
Answer: A: How to get coordinates from UCSC Genome Browser
... When you enter the gene name genome browser offers you with a list of genes and transcripts that match your query, each one has the coordinates for the assembly that you selected.  Alternatively you can go to Table browser and download a flat table that you can customize:https://genome.ucsc.edu/cgi ...
written 3.6 years ago by Gian350
1
vote
3
answers
1.4k
views
3
answers
Answer: A: Looking for clean list of gene names for UCSC's HG19
... You can download and customize a table at Table Browser on UCSC website   https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=454476929_Suu1xE8YJzeT7c2Q2Aweg5CZL48p&clade=mammal&org=Human&db=hg19&hgta_group=allTracks&hgta_track=knownGene&hgta_table=0&hgta_regionType=genome&a ...
written 3.6 years ago by Gian350
1
vote
1
answer
3.5k
views
1
answers
Comment: C: Heatmap Column Side Color question in R
... Hi Afshin, The idea here is to have two different data frames, one with your heatmap data(ex expression data) and the other with the annotation for the patients. Instead of changing the header of your 'dummymat' you should add a column in 'categories' for the characteristic that you want to plot. ...
written 3.6 years ago by Gian350
1
vote
1
answer
3.5k
views
1
answers
Comment: C: Heatmap Column Side Color question in R
... The colors are different because pheatmap doesn't create symmetric breaks, to achieve that you can specify the breaks (last line): pheatmap(dummymat, color = bluered(800), clustering_method = "mcquitty",          clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean",       ...
written 3.6 years ago by Gian350
0
votes
1
answer
3.5k
views
1
answers
Comment: C: Heatmap Column Side Color question in R
... Please always use a reproducible example so other people can run it and help. Try to use the 'dummymat' I posted instead of 'x' and 'colnames(expr_mat)'   ...
written 3.6 years ago by Gian350

Latest awards to Gian

Supporter 3.6 years ago, voted at least 25 times.
Scholar 3.6 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph
Scholar 3.6 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph
Scholar 3.8 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph
Scholar 3.9 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph
Scholar 4.8 years ago, created an answer that has been accepted. For A: Creating subgraph using igraph
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Creating subgraph using igraph

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1021 users visited in the last hour