User: ashish

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ashish570
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Posts by ashish

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Comment: C: downloading of datasets for construction of a model pathway
... He is probably talking about genome scale metabolic network since that is the systems biology approach for reconstruction/modelling of pathways. You would need a lot more than just expression datasets to achieve that. ...
written 11 weeks ago by ashish570
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Comment: C: How to identify which genes are responsible for the different cluster without P
... Is there a specific reason why you do not want to do PCA, it sounds like a good job for PCA. You can also visualize loadings plot using [PCATools][1] package. It is pretty easy to make [1]: https://bioconductor.org/packages/release/bioc/vignettes/PCAtools/inst/doc/PCAtools.html ...
written 4 months ago by ashish570
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Comment: C: Issue installing rmats using conda
... I have rmats installed in a separate environment and it uses python 3.7. ...
written 4 months ago by ashish570
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Comment: C: Issue installing rmats using conda
... Make a separate environment and install rmats in it. Avoiding these conflicts by making separate environments is the whole point of using conda. ...
written 4 months ago by ashish570
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Comment: C: DESeq2 and DEXSeq
... There are no programs which can incorporate both deseq and dexseq according to my knowledge. However, if you are interested in splicing I would suggest junctionseq instead of dexseq. ...
written 4 months ago by ashish570
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Comment: C: DESeq2 and DEXSeq
... DESeq2 is for differential gene expression and DEXSeq is for differential exon usage. Both are different things. What is your aim here? ...
written 4 months ago by ashish570
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Comment: C: How to a make schematic picture for RNA-seq steps
... I cannot see the picture but if you want to do this in R then use the package diagrammeR. [Here][1] is a short tutorial to get you started. [1]: https://datascienceplus.com/how-to-build-a-simple-flowchart-with-r-diagrammer-package/ ...
written 4 months ago by ashish570
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Comment: C: Finding common and different genes between species
... Are these plants related? You may look at presence/absence variation tools. These are part of pangenome/transcriptome analysis methods. Here is one [approach][1]. [1]: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6174-3 ...
written 6 months ago by ashish570
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Comment: C: calculating fold change
... How did you get this list of differentially expressed genes? ...
written 6 months ago by ashish570
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Answer: C: Downloading gene sequences for a list of genes using E-utilities
... Most probably these are ids from Oryza sativa indica which is a different sub-species than the one we see more often (japonica). It was sequenced by BGI, China and the assembly is [available][1] at ensembl plants which can be accessed using biomart. However, BGI has sequenced many other plants and w ...
written 6 months ago by ashish570

Latest awards to ashish

Popular Question 9 weeks ago, created a question with more than 1,000 views. For infer sub-families from phylogenetic tree
Student 4 months ago, asked a question with at least 3 up-votes. For levels in gene ontology
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Avoid repetition in script
Popular Question 9 months ago, created a question with more than 1,000 views. For infer sub-families from phylogenetic tree
Teacher 10 months ago, created an answer with at least 3 up-votes. For C: How to convert .tar file to fasta file?
Popular Question 10 months ago, created a question with more than 1,000 views. For orthologue mapping using circos
Popular Question 11 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 11 months ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Great Question 11 months ago, created a question with more than 5,000 views. For retrieving best hit in local blast output
Great Question 14 months ago, created a question with more than 5,000 views. For heatmap using FPKM values
Great Question 15 months ago, created a question with more than 5,000 views. For levels in gene ontology
Centurion 16 months ago, created 100 posts.
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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Is this RNA-seq data reliable?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Gap treatment in MEGA for ML phylogeny
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.1 years ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 2.4 years ago, created a question with more than 1,000 views. For blastn for very short sequences
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.4 years ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Problem building reference genome using STAR
Popular Question 2.8 years ago, created a question with more than 1,000 views. For retrieving best hit in local blast output
Popular Question 3.0 years ago, created a question with more than 1,000 views. For how to analyse gene expression using RNA-seq data
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