User: EagleEye

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EagleEye4.9k
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Sweden
Website:
https://www.researchga...
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gridhrahakshi
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Last seen:
14 hours ago
Joined:
3 years, 5 months ago
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 794 results • page 2 of 80 • next >
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Answer: A: creating a heatmap with R and retrieve cluster data from dendogram
... For extracting clusters from generated heatmap/dendogram check this [previous post][1]. [1]: https://www.biostars.org/p/264268/#264303 ...
written 4 weeks ago by EagleEye4.9k
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Answer: A: How to identify and count multi-exon genes
... I assume you want to identify multi-exon transcripts from your GTF file. I hope this [post][1] will help you making table with number of exons per transcript. [1]: https://www.biostars.org/p/248210/#248235 ...
written 4 weeks ago by EagleEye4.9k
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Answer: A: How to get each exon counts from TCGA
... Hi, Try Synapse project, https://www.synapse.org/#!Synapse:syn300013/files/ ...
written 4 weeks ago by EagleEye4.9k
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Answer: A: KEGG pathways and modules
... Try GeneSCF. ...
written 6 weeks ago by EagleEye4.9k
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Answer: A: Gene ontology and KEGG pathway analysis of rice RNA-seq data
... Try [GeneSCF][1]: **For 'Oryza sativa japonica (Japanese rice) (RefSeq)' from KEGG: osa** ./prepare_database -db=KEGG -org=osa ./geneSCF -m=normal -i=INPUTgene.list -t=sym -db=KEGG -o=/ExistingOUTPUTfolder/ -org=osa --plot=no --background=#num_genes Alternate: **For 'Oryza sativa japoni ...
written 8 weeks ago by EagleEye4.9k
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Answer: A: Generating cluster heat map
... I would recommend [ComplexHeatmap][1] (comes with more functionality). Check my previous post for [simple example code][2]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s2.single_heatmap.html [2]: https://www.biostars.org/p/264268/#264303 ...
written 8 weeks ago by EagleEye4.9k
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Answer: A: Time course experiment in RNASeq
... http://www.cs.cmu.edu/~jernst/stem/ ...
written 8 weeks ago by EagleEye4.9k
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Comment: C: Perfoming functional enrichment of DEGS
... Hi, It depends on what biological question you are trying to address. ...
written 9 weeks ago by EagleEye4.9k
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Answer: A: Visualization of Gene Ontology using bubble plot.
... Check out [GeneSCF][1] Representation figures in GeneSCF article: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1250-z [1]: https://www.biostars.org/p/108669/ ...
written 9 weeks ago by EagleEye4.9k
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Answer: A: The web page at ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra
... You can alternately download directly from the ENA deposit (PRJNA299026, GSE74112), https://www.ebi.ac.uk/ena/data/view/SRP064924 1) Download the text file generated from ENA/SRA 2) Use the links (column: **FASTQ files (FTP)**) from the text file to download compressed fastq file (*fastq.gz) (I p ...
written 9 weeks ago by EagleEye4.9k

Latest awards to EagleEye

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Epic Question 5 months ago, created a question with more than 10,000 views. For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to look up GO terms in BioMart using GI ID or Accession ID
Scholar 5 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 6 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 7 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Scholar 8 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Appreciated 8 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Appreciated 8 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA

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