User: EagleEye

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EagleEye4.8k
Reputation:
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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, 3 months ago
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Investigating field of biology by applying logics of computer science, statistics and mathematics.

Posts by EagleEye

<prev • 780 results • page 1 of 78 • next >
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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 21 hours ago by EagleEye4.8k
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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 2 days ago by EagleEye4.8k
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Answer: A: Time course experiment in RNASeq
... http://www.cs.cmu.edu/~jernst/stem/ ...
written 4 days ago by EagleEye4.8k
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Comment: C: Perfoming functional enrichment of DEGS
... Hi, It depends on what biological question you are trying to address. ...
written 7 days ago by EagleEye4.8k
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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 days ago by EagleEye4.8k
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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 12 days ago by EagleEye4.8k
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Answer: A: How to get Kegg pathway names from kegg pathway IDs
... [GeneSCF][1] 'prepare_database' module downloads KEGG-ID, description and genes associated with the terms as simple table format (plain text file). ./prepare_database -db=KEGG -org=mmu The above command downloads complete KEGG db as simple text file in following location, 'geneSCF-tool/class/l ...
written 16 days ago by EagleEye4.8k
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Answer: A: hisat2 library type
... You might have to just connect these dots. **Library type info (Double check which protocol was used for sequencing):** http://onetipperday.sterding.com/2012/07/how-to-tell-which-library-type-to-use.html **HISAT2 info:** For single-end reads, use F or R. 'F' means a read corresponds to a ...
written 23 days ago by EagleEye4.8k
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Comment: C: Many Differentially expressed genes but few GO terms
... Need some more details. Choice of tool matters depending on the type of organism you are looking for. 1) What are the tools you used. 2) Parameters used in individual tool. ...
written 23 days ago by EagleEye4.8k
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Comment: C: GeneSCF (Gene Enrichment Tool): Advice to users
... Hi, Please provide sample of your input file and output files (including 'gi_3652_user_mapped.list'). **Tip:** When you run 'prepare_database' before running 'geneSCF', you do not have to run 'geneSCF' in update mode (since you just updated with 'prepare_database'). ...
written 24 days ago by EagleEye4.8k

Latest awards to EagleEye

Appreciated 1 day ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Epic Question 3 months ago, created a question with more than 10,000 views. For Gene Set Clustering based on Functional annotation (GeneSCF)
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Scholar 3 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Scholar 4 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to check the type of identifier from ensembl?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Appreciated 5 months ago, created a post with more than 5 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: Clinical Survival data of TCGA
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Something better than GSEA?
Scholar 6 months ago, created an answer that has been accepted. For A: How to interpret the result of GO analysis using Ontologizer ?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Clinical Survival data of TCGA
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to check the type of identifier from ensembl?
Teacher 6 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

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