User: newscient

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newscient0
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Posts by newscient

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Comprehensive gene annotation for drosophila melanogaster
... Is there a trustworthy and so-called comprehensive annotation for drosophila melanogaster of all genomic regions in order to construct a TSS (transcription start site) database? Is it UCSC (by quering), modENCODE, flybase or ensembl that i should search for it? I am looking for something like the G ...
genome written 12 weeks ago by newscient0 • updated 12 weeks ago by Jean-Karim Heriche13k
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Comment: C: Homology percentage for different species query
... You are right and i clarify. So i am not talking about the sequence similarity neither.When i am saying "homology percentage" , i mean the ratio : protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism. x 100 :-) ...
written 2.5 years ago by newscient0
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Homology ratio comparison between different species
... I found the homology ratio* for all protein coding genes between several organisms and mouse using a phylogenetic-based approach. I have noticed that the ratio found between an organism and mouse is greater than the ratio between another organism and mouse! On the other hand the second is evolutiona ...
homology evolutionary distance written 2.5 years ago by newscient0
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Comment: C: How to get gene names from CpG islands coordinates with R/Bioconductor
... I guess i have to make a mapping of my CpG coordinates with a mouse gene annotation, that's what i am missing, right? And then find the gene_ids from there! ...
written 2.5 years ago by newscient0
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How to get gene names from CpG islands coordinates with R/Bioconductor
... I have a dataframe with chromosome name , start position, end position (only! no other identifier) of CpG islands from the mouse genome (mm10 coordinates).  Is there a function with which i can retrieve the related ensembl gene ids? I suppose getBM from the bioMart package would do the job , but ho ...
annotation cpg written 2.5 years ago by newscient0 • updated 2.5 years ago by Martin Morgan1.5k
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Comment: C: True/False Positives/Negatives in R
... Yes your point about the control dataset is totally correct! But the genes "without peaks" will be the rest of the organism's genes which i also find meaningless, so i will stick with the discarded ones! Thanks again ...
written 2.5 years ago by newscient0
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Comment: C: True/False Positives/Negatives in R
... Thanks for your quick answer, As a neg_exp dataset (genes not regulated by the complex according to my experiment) could be the genes that i discarded during the Chip-seq data analysis by filtering, right? ...
written 2.5 years ago by newscient0
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True/False Positives/Negatives in R
... I have made a database of genes from different organisms found as regulated by a specific protein complex through Chip-Seq data analysis.I also have a positive control for all these organisms(genes that have been found to be regulated by the complex) and a negative control for all the organisms (gen ...
R analysis chip-seq condition testing written 2.5 years ago by newscient0 • updated 2.5 years ago by Devon Ryan70k
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Comment: C: Iterate with getBM(bioMart package) for GO annotation
... Right..-.-"! Thanks  ...
written 2.6 years ago by newscient0
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Iterate with getBM(bioMart package) for GO annotation
... I am trying to use the getBM function for a list of dataframes(or datasets if you prefer) (genes2peaks) and use only a list of gene_ids from there and get the GO annotations for each dataset seperately in a new list, but i get only annotations for the final dataset in my list! I also retrieve the c ...
gene ontology getbm iteration written 2.6 years ago by newscient0 • updated 2.6 years ago by Devon Ryan70k

Latest awards to newscient

Popular Question 2.5 years ago, created a question with more than 1,000 views. For Homology ratio comparison between different species
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to get gene names from CpG islands coordinates with R/Bioconductor
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Iterate over Rangeddata in R with a for loop
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to write a list of DNAStringsets as a FASTA file in R
Popular Question 2.5 years ago, created a question with more than 1,000 views. For True/False Positives/Negatives in R

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