User: carina2817

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carina281720
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Posts by carina2817

<prev • 15 results • page 1 of 2 • next >
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How to create partial dependence plots for multinomial gbm in R?
... Hello, I am trying to create partial dependence plots for my multinomial gbm predictions but I haven't been able to figure out how to produce the correct plots, the ones that I am getting have a single line instead of a line for every level of my response variable (in my case are 3 different specie ...
multinomial R gbm partial-dependence-plot pdp written 9 weeks ago by carina281720
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How to get the response variable from gbm model when train.fraction is <1 ?
... Hello, I am running gbm function (from GBM R package) and I am setting the option train.fraction to 0.7. I would like to get a vector with the response variable corresponding to this subset. I though this must be saved in one of the variables of the output gbm object but I haven't found it and I do ...
R gbm response training written 10 weeks ago by carina281720
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Comment: C: Problem to improve GBM (gradient boosting) model in r
... Thank you! I am gonna try with LightGBM ...
written 10 weeks ago by carina281720
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Problem to improve GBM (gradient boosting) model in r
... Hello, I am trying to test different parameters in the function gbm of R in order to make predictions with my data . I have a huge table of 79866 rows and 1586 columns where columns are counts for motifs in the DNA and rows indicate diferent regions/positions in the DNA and the organism to which ...
R predictions gbm test written 11 weeks ago by carina281720 • updated 11 weeks ago by zx87549.2k
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How to get Motif positions by peak (not by Chromosome) using Homer annotatePeaks.pl ??
... Hello, I would like to get positions of motifs (start and end positions) for the motifs found in every peak using annotatePeaks.pl of Homer. I tried the following: annotatePeaks.pl ad_close.bed Aque1.31 -m knownResults/*.motif -gff3 Aqu2.1_Genes.gff3 -mbed motifs.bed > motifs.tsv The outp ...
homer annotatepeaks peakid positions motif written 3 months ago by carina281720
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Comment: C: Homer software -size parameter
... Hello, I am trying to understand how Homer chooses the center of the peak when I don't specify size, do you know if '-size given' is the default? I want to get positions for the motifs found in the peaks but the output does not look like the center of the peak is litterally the middle point of the ...
written 3 months ago by carina281720
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Comment: C: Error running OrthoMCL
... Dear Jean, I am having the same problem with memory. I ran orthoMCL-pipeline to run orthoMCL in an easier way but I have a lot of data and I was following a tutorial so I guess It was my mistake not clearing temporal files. Do you know how I could continue the process without loosing the progress? I ...
written 5 months ago by carina281720
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Comment: C: Which software is suitable for protein prediction from whole eukaryotic genomes?
... The gff file looks like this: gff-version 3 !gff-spec-version 1.21 !processor NCBI annotwriter !genome-build ASM263302v1 !genome-build-accession NCBI_Assembly:GCA_002633025.1 sequence-region NMRB01000001.1 1 1576180 species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=416868 NMRB0100 ...
written 7 months ago by carina281720
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Comment: C: Which software is suitable for protein prediction from whole eukaryotic genomes?
... Hi, thank you for your answer. I am trying to understand how to get proteomes using gff files (I found this files for some of my species). I read a post where someone was asking how to do this (https://bioinformatics.stackexchange.com/questions/6865/can-a-gff-file-be-converted-to-a-fasta-file) and s ...
written 7 months ago by carina281720
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Which software is suitable for protein prediction from whole eukaryotic genomes?
... Hello, I want to try programms for Orthologous prediction (OrthoMCL for example), the programs work with proteomes but I have some genomes of eukaryotic organisms for which I don't have proteomic data, Could you please recomend me some software to predict protein sequences from whole genomes? ...
eukaryotic genome protein prediction written 7 months ago by carina281720 • updated 7 months ago by gb1.8k

Latest awards to carina2817

Scholar 7 months ago, created an answer that has been accepted. For A: How to solve the different number of hits from tblastn when I use the option -pa

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