User: andres.firrincieli

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Posts by andres.firrincieli

<prev • 126 results • page 1 of 13 • next >
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Answer: A: Is a compositional bias in Sequence Content of initial bases in WES reads normal
... I am not a WES expert but that is pretty normal for [RNA-seq data][1] [1]: https://www.biostars.org/p/179565/ ...
written 10 hours ago by andres.firrincieli630
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Answer: C: differentially coexpressed genes using wgcna?
... Hi, most of the time you get modules from WGCNA but that does not mean that your modules are biologically meaningful. Look at the heatmap of each modules and the check if the gene expression profile changes across your main conditions ...
written 1 day ago by andres.firrincieli630
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Answer: A: how to annotate draft genome
... As Mensur said GTDB can be used to determine taxonomic affiliation of your bins. In case you do not have 128 Gb of RAM, GTDB has been implemented in [KBase][1] [1]: https://kbase.us/applist/apps/kb_gtdbtk/run_kb_gtdbtk/release ...
written 17 days ago by andres.firrincieli630
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Answer: A: Gene enrichment analysis for metagenome (non-model organisms)
... Hi Tom, for GO enrichment analysis you could use [topGO][1] [1]: https://bioconductor.org/packages/release/bioc/html/topGO.html ...
written 22 days ago by andres.firrincieli630
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Comment: C: Gene count vs Relative gene abundance
... not really. They did not assembled the metagenome: > An average of 34.1 million paired-end reads were produced for each > sample and, after removing human contamination (∼0.1%, on average), > 19.9 ± 6.7 million reads were mapped at a unique position of the reference catalogue of 3.3 milli ...
written 25 days ago by andres.firrincieli630
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Comment: C: Extracting Genes that contribute to 1st PC
... The `rownames` of `intramodularconnectivity` should have the `gene_id`. Could you attach the chunck of code used to prepare `datExpr`? ...
written 29 days ago by andres.firrincieli630
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Answer: A: Extracting Genes that contribute to 1st PC
... Hi reara, With signed netwroks, In WGCNA the genes that mostly contributes to the 1st PC are the ones with the highest Module Membership or Intramodulat Connectivity For Unsigneed networks, the genes that mostly contributes to the 1st PC are the ones with the highest absolute value of Module Memb ...
written 29 days ago by andres.firrincieli630
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Comment: C: DESeq results based on lfcthreshold
... Hi BS, here is the reason why the number of DEG drop if you rise the lfcthreshold: [link][1] [1]: https://support.bioconductor.org/p/101504/ ...
written 5 weeks ago by andres.firrincieli630
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Comment: C: Heatmap of mothur output with Phyloseq
... What is the output of `head(stability.paired.trim.contigs.unique.good.filter.unique.precluster.pick.pick.opti_mcc.0.03.cons.taxonomy)` and `tax_table(physeq)` ...
written 6 weeks ago by andres.firrincieli630
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Comment: C: Heatmap of mothur output with Phyloseq
... you can't use `head()` on a S4 object. To inspect the OTU table simply use `otu_table(physeq)`. For the taxonomy `tax_table(physeq)`. [Source][1] [1]: https://joey711.github.io/phyloseq/preprocess.html ...
written 6 weeks ago by andres.firrincieli630

Latest awards to andres.firrincieli

Centurion 3 months ago, created 100 posts.
Scholar 3 months ago, created an answer that has been accepted. For A: Correlating WGCNA modules to Diseased/Not-Diseased Trait
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
Scholar 5 months ago, created an answer that has been accepted. For A: Correlating WGCNA modules to Diseased/Not-Diseased Trait
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Non-computational challenges in bioinformatics
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
Scholar 11 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 11 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 11 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu

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