All Questions
14 questions
-5
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0
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18
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How to find hub genes when your input DEGs are more than 4000 because it takes so long to calculate modules
I tried extracting 250 hub genes from 4750 DEGs, but it takes too much time while calculating modules from 11 methods and coudn't proceed further.
1
vote
0
answers
21
views
Find most abundant transcript isoform of a gene across different tissues in long read RNA-Seq data
I want to understand which is the most abundant variant of a gene of interest across different tissues by looking at different publicly available databases (mouse/human). I have deduced from ...
- 133
0
votes
1
answer
56
views
Target genes for piRNA
Where I can find a database or tool to give me the target genes of PIWI (piRNAs) in human?
I found one but works for worm like <...
- 2,232
1
vote
1
answer
387
views
Differential gene expression analysis of time series with replicates
I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8 time points. How do we do Differential gene expression analysis to find significantly ...
0
votes
2
answers
374
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Problem with merge data while trying to convert gene names in R
This question has also been asked on Biostars and StackOverflow
I've been trying to code (in R) a way to convert gene accession numbers to gene names (from RNAseq data). I've looked at all the related ...
- 129
1
vote
1
answer
713
views
Clustering of gene co-expression network by igraph R package
I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges.
The network file as an edge list format of memory around 1gb ...
2
votes
1
answer
74
views
How can I interpret gene expression data from Bioconductor packages?
I am currently looking at microarray data from a bioconductor microarray dataset. Specifically, I have data (a snippet) which looks like the following:
...
- 21
1
vote
3
answers
4k
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How to quantile normalization on RNA seq counts
I have a read count data (RNAseq) and want to perform quantile normalization. Could you please help me how to do it. I tried some scripts in R but it didn't work. I want the result output in matrix ...
- 351
3
votes
3
answers
327
views
How to visualize genome track of gene in specific cell-lines?
I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data.
It should look something like this I have recently seen this encode, but in ...
- 1,272
0
votes
3
answers
770
views
How to find correlation between two specific genes in same dataset?
I would like to plot the correlation between two specific genes in my data. I have a matrix with genes in rows and samples in columns, with read counts data. If I want to look at the correlation ...
- 631
4
votes
3
answers
513
views
Expression of a gene in different groups
I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not.
From this paper lncRNA ...
- 631
9
votes
3
answers
3k
views
How to identify gene expression signatures from gene expression data?
I have TCGA gene expression data. I'm interested in identifying gene expression signatures using the data.
I would like to know whether there are any tools or R packages for identifying gene ...
- 1,272
3
votes
1
answer
298
views
How to download gene expression data from NCBI gene database
In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
- 31
2
votes
1
answer
73
views
Get gene annotation type from gene name
I am having RNA-seq data set for C.Elegans. I do not know which annotation scientists used for naming the genes of it, but I ...
- 2,578