User: enxxx23

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enxxx23240
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Posts by enxxx23

<prev • 52 results • page 2 of 6 • next >
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Answer: A: chimeric transcripts detection tool
... FusionCatcher https://sourceforge.net/projects/fusioncatcher/ ...
written 2.2 years ago by enxxx23240
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Answer: A: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... I would answer like this to non-bioinformatician or non-statistician. EdgeR, DESeq2, Limma, and so on are different methods (which use complex statistics) and therefore one would expect when using different methods to get different results. Indeed there is some similarity at general/conceptual leve ...
written 2.2 years ago by enxxx23240
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Comment: A: Gene Set Enrichment Analysis after DESeq2
... I like DESeq2. It would be great to have in the future something like ROAST/CAMERA/GSEA in DESeq2 too! ...
written 2.2 years ago by enxxx23240
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Comment: C: Evaluate single cell data to look at combinations of gene expression within sing
... Using WGCNA requires at least 20 samples. Also WGCNA analysis is not "stable", which means that the another researcher will find impossible to reproduce the results of WGCNA analysis without having the original script where the WGCNA analysis was done. Also at a close inspection it looks like may mo ...
written 2.2 years ago by enxxx23240
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Comment: C: RNAseq with quantseq
... I meant that is there any reference (e.g. scientific article and not markerting material) which supports this? Do the authors of edger, limma, or DESeq2 concur with this? ...
written 3.4 years ago by enxxx23240
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Comment: C: RNAseq with quantseq
... Does R packages like edgeR, limma, DESeq2 work with QuantSeq 3' RNAseq? I mean, has anybody used and published results based on QuantSeq data analyzed with edgeR, limma, DESeq2? ...
written 3.4 years ago by enxxx23240
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Comment: C: Gene Fusion Detection: Rna-Seq Data
... Actually, Tophat-fusion and STAR-fusion need a lot of improvement. Tophat-fusion consistently in is the bottom of all comparisons of fusion finders. TopHat-fusion calls hundreds of thousands of fusions per sample when it is well known that fusions are very rare and one has one fusion for every 10 sa ...
written 3.7 years ago by enxxx23240
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Answer: A: List of known fusions
... It is not clear what kind of fusions are you looking for. Are you looking for fusions which are known also in healthy people, like for example MSMB-NCOA4, TTY15-USP9Y, SLC45A4-ELK4? Here are very few: http://54.84.12.177/PanCanFusV2/ http://203.255.191.229:8080/chimerdbv31/mindex.cdb For example, ...
written 3.9 years ago by enxxx23240
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Comment: C: When Aligning Mirna (Micro Rna) What Reference Is Better? (Whole Genome Or Mirba
... So according to the articles/pre-prints where Salmon and Kallisto have been published, Salmon and Kallisto are mapping/aligning reads on transcriptome. Indeed there are many types of aligments/mappings, like for example pseudo-alignment or pseudo-mapping but this is a sub-type of alignment/mapping ...
written 3.9 years ago by enxxx23240
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Answer: A: When Aligning Mirna (Micro Rna) What Reference Is Better? (Whole Genome Or Mirba
... I would recommend to align the reads on all miRNAs because the reads are coming from miRNAs. miRNA is even in the title of miRNA-seq. The equivalent for RNA-seq is to align the reads on all RNAs (that is the transcriptome) as tools as Kallisto and Salmon are doing. It it not a good idea to align mi ...
written 3.9 years ago by enxxx23240

Latest awards to enxxx23

Popular Question 2.8 years ago, created a question with more than 1,000 views. For Public RNA-seq dataset for human & 2x250bp or longer
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: The new era of bioinformatics: simple and fast tools, fewer and more informative
Commentator 6.1 years ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologists are reinventing the wheel for

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