User: asmariyaz23

gravatar for asmariyaz23
asmariyaz2310
Reputation:
10
Status:
New User
Location:
United States
Last seen:
2 hours ago
Joined:
5 years, 7 months ago
Email:
a**********@gmail.com

about me

Posts by asmariyaz23

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
47
views
0
answers
Plot features on tsne plot with high pLi scores
... Hello, I have used Seurat to obtain tsne plot and calculated the DE genes for each cluster. I have pLi scores for each of these DE genes and I want to somehow plot the genes that have pLi score >=0.9 on them. Using FeaturePlot in Seurat I could do 1 gene per plot but I was wondering if there is ...
pli genes tsne rna-seq seurat written 9 days ago by asmariyaz2310 • updated 2 days ago by Biostar ♦♦ 20
0
votes
1
answer
167
views
1
answers
Comment: A: Gene set enrichment analysis using a curated gene list and cluster DE genes
... I will try it this way as well, just needed clarification on 2 variables N and k. N = Are these the total number of genes in matrix (after initial filtration in a single cell package, in my case Seurat)? k = Here do you refer to only the DE expressed genes in the cluster of interest or the total ...
written 8 weeks ago by asmariyaz2310
2
votes
1
answer
167
views
1
answer
Gene set enrichment analysis using a curated gene list and cluster DE genes
... I have a curated gene list using which I would like to carry out enrichment analysis on DE genes in clusters obtained using Seurat. I first tried to do this manually using Fisher Exact test like so: No. genes in curated list: 5840 No. DE genes in Cluster 0 (from Seurat): 512 No. Over ...
enrichment rna-seq R written 8 weeks ago by asmariyaz2310
0
votes
1
answer
191
views
1
answers
Answer: A: Seurat cluster is split and appears in 2 different areas on the tsne plot
... I have been trying to play with tsne parameters as you suggested, mainly max.iter, min_dist and n_neighbors. For some reason it is the 13th cluster which splits up and occurs in 3 different locations. Image in link below. Is there some other parameter that I should explore? ![enter image descriptio ...
written 10 weeks ago by asmariyaz2310 • updated 10 weeks ago by i.sudbery5.3k
0
votes
1
answer
191
views
1
answer
Seurat cluster is split and appears in 2 different areas on the tsne plot
... Hello, I am analyzing a single cell dataset using Seurat. The tsne plot obtained shows the same cluster in 2 different locations. I am wondering if I should be merging them or play with the parameters for tsne to separate them out further. To study these 2 clusters I want to look into the genes in ...
R tsne seurat cluster_analysis written 10 weeks ago by asmariyaz2310
0
votes
1
answer
2.1k
views
1
answers
Answer: A: Converting Between Mass-Spec Database Search Result Formats (Specifically Pep.Xm
... I don't know too much about R but Python's XML parser does an excellent job in doing what you want. Once you know the fields within this id.csv file that ISOBAR accepts, extract the information with the parser, store them as lists and push them to a writing file, Please ignore this post if Python i ...
written 5.5 years ago by asmariyaz2310
0
votes
1
answer
1.2k
views
1
answer
Newick Tree Reordering
... I have a newick tree which I need to reorder in a certain order. I am trying to use MEGA for this purpose but since the tree is huge its getting to difficult to reorder? Is there any other option to do the same? ...
written 5.5 years ago by asmariyaz2310 • updated 5.5 years ago by har-wradim20
0
votes
1
answer
6.7k
views
1
answers
Comment: C: Convert Distance Matrix To Newick Format- Biopython
... I got a tree with your program. However, I had to avoid the organism names and make data matrix out of numerical values alone. However I face a problem when I need to make a heat map out of such a tree.With the use of "Tree" and Profileface (which is used for heatmap) in ETE2 package, I tried making ...
written 5.6 years ago by asmariyaz2310
2
votes
1
answer
6.7k
views
1
answer
Convert Distance Matrix To Newick Format- Biopython
... Need to make a plot merging heat map and a phylogenetic tree in Python. I have already made the heat map using the square distance matrix that I have with the help of numpy and matplotlib but now I would like to merge a phylogentic tree with this heat map, For this purpose I found a BioPython Packag ...
python phylogenetics distance written 5.6 years ago by asmariyaz2310 • updated 5.6 years ago by jhc2.8k

Latest awards to asmariyaz23

Great Question 4.1 years ago, created a question with more than 5,000 views. For Convert Distance Matrix To Newick Format- Biopython
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Newick Tree Reordering
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Convert Distance Matrix To Newick Format- Biopython

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 750 users visited in the last hour