User: pengchy

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pengchy410
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Posts by pengchy

<prev • 103 results • page 1 of 11 • next >
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Answer: A: Package to classify LncRNA into LncRNAs, intronic LncRNAs and antisense LncRNAs
... Please have a look at [`gffcompare`][1], through which genomic gff file could be used as reference ("-r"). [1]: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml ...
written 6 months ago by pengchy410
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Comment: C: How To Interpret The Results Produced By Verify3D Structure Evaluation Server?
... The new web service of Verify 3D is available [here][1] [1]: http://servicesn.mbi.ucla.edu/Verify3D/ ...
written 10 months ago by pengchy410
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stand-alone pre-miRNA prediction packages
... Hi, after a while searching and investigation, I couldn't found a user-friendly available package for pre-miRNA prediction or classification, although large number of this kind of packages have been published since 2003. The following packages have been tested failed. - Triplet-SVM: Need contact t ...
prediction pre-mirna stand-alone package written 12 months ago by pengchy410
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Comment: C: Problem ViennaRNA package install
... Please provide the full log information of "configure" and "make". ...
written 12 months ago by pengchy410
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Answer: C: Alternative tools for PacBio collapse_isoforms_by_sam.py
... This problem has been resolved by installation of: [cDNA_Cupcake][1], which is easy to install and also contains collapse_isoforms_by_sam.py script [1]: https://github.com/Magdoll/cDNA_Cupcake/wiki ...
written 17 months ago by pengchy410
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Alternative tools for PacBio collapse_isoforms_by_sam.py
... Dear all, During the PacBio full length transcriptome data analysis process, one step is to collapse the sam files to get the unique isoform structure using collapse_isoforms_by_sam.py scripts. This script can be run from smrtlink package. However, the installation of smrtlink need root authority t ...
sam pacbio collapse written 17 months ago by pengchy410
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more transcriptional factors involved lead to quick or slow phenotype transition?
... As the title says. I have found that one phenotype transition has more TF genes involved while the reverse process need less TFs. Also, these two processes have different rates of transition. So, I wonder if there was any papers describing the relationship between the number of involved TFs and the ...
transcriptional factors phenotype transition written 18 months ago by pengchy410
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Comment: A: Parkinson disease databases
... 1. You could check several review papers of the transcriptome analysis: Redensek, S., et al. (2018). "From Genomics to Omics Landscapes of Parkinson's Disease: Revealing the Molecular Mechanisms." OMICS 22(1): 1-16. Borrageiro, G., et al. (2018). "A review of genome-wide transcriptomics studies in ...
written 19 months ago by pengchy410
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Comment: C: Novel MicroRNA prediction with Mirdeep 2.
... From the pdfs produced by miRDeep2, you can found that the miRDeep2 score were broken into several parts, including score for star reads, score for read counts, score for mfe, score for randfold, and score for cons. seed. Among of them, score for read counts always are the maximum. So, I speculate t ...
written 22 months ago by pengchy410
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Comment: C: Misleading mirDeep2 output? recall not tallying
... Indeed, the documentation for miRDeep output files are very little. From miRDeep2 paper (NAR, 2012), the authors said that "For each score cut-off the sensitivity and number of true positive novel miRNAs is estimated". According to this sentence, the number of true positive novel miRNAs is estimated ...
written 22 months ago by pengchy410

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