User: Macherki M E

gravatar for Macherki M E
Macherki M E120
Reputation:
120
Status:
Trusted
Location:
Tunisia/ksour essef
Twitter:
EMacherki
Last seen:
1 year, 5 months ago
Joined:
3 years, 3 months ago
Email:
m*******************@live.fr
Amator in bioinformatics and I usually use R as programming language. I am working to make a catalog of functions with sample implementation and clear algorithms. I look for contribution if someone like.

Posts by Macherki M E

<prev • 21 results • page 1 of 3 • next >
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Answer: A: How to reorder dendrogram (R)?
... I thinks that the dendrogram had the some order of user matrix input. In that way user will control the position of each vertice. If you wont separate a specific class statistically based on distance or graphically we have to reformulate data input. ...
written 2.5 years ago by Macherki M E120
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Comment: C: Peaks in GC% histogram
... It's clear from the histogram that a duplication was occurred, but the significance of this observation is correlate with data.Can you add details, length of sequence an the method used: as a stream or with fixed windows. ...
written 2.6 years ago by Macherki M E120
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Comment: C: How to make Phylogenetic tree on R
... If you have the distance matrix, my be from bibliography you can create your cluster. The basic is hclust which requires a distance object ,created generally from a matrix. For more details you can see the help for hclust and dendrograme ...
written 2.6 years ago by Macherki M E120
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Comment: C: problems on hierarchical clustering
... I think that the function required a list with more then two elements. It's clear by the stopifnot closure, try to pass each integer as list element using vector function ! ...
written 2.6 years ago by Macherki M E120
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Comment: C: counting motifs in dna sequence
... Biostrings package in R provides a beautiful function for you purpose:gregexpr2 ...
written 2.9 years ago by Macherki M E120
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Comment: C: Clustering using codon usage similarity
... I confirm the first comment but we shoold respect the distance object forma ...
written 2.9 years ago by Macherki M E120
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Comment: C: Generate random genomic positions with R
... You need a random position .may be with sample(1:length sequence,1,true) will gives one sample ...
written 2.9 years ago by Macherki M E120
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Comment: C: Best way to normalize occurance of a nucleotide subsequence
... A think yes. Is just a simple algebra. You can also use the reverse complement to your sequence,your sample will more extinded see karlin s. works. ...
written 2.9 years ago by Macherki M E120
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Answer: A: Best way to normalize occurance of a nucleotide subsequence
... Rho index is a generic function calculation in bioinformatics. kralin S. report that the abundance shame of a subsequence can be calculated using the Probability of independent evens: P(ab)=P(a)*P(b) ===> P(ab….n)=P(a)*P(b)*…P(n) Rho is set as the ratio between join evens `"ab..n"` and ...
written 2.9 years ago by Macherki M E120
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Comment: C: Best way to normalize occurance of a nucleotide subsequence
... The Rho is absolute calculation of independency between a sequence with alphabet z. As i know ,you can edit the alphabet in the sequence. Missing value takes absolutly p=1. For other upac use the sum of letters frequency. Try then to modify the rho function to get setting options. ...
written 2.9 years ago by Macherki M E120

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Popular Question 21 months ago, created a question with more than 1,000 views. For k-mer counting into R using perfect hashing
Supporter 2.6 years ago, voted at least 25 times.
Scholar 2.9 years ago, created an answer that has been accepted. For A: k-mer counting into R using perfect hashing
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Scholar 3.0 years ago, created an answer that has been accepted. For A: k-mer counting into R using perfect hashing
Student 3.0 years ago, asked a question with at least 3 up-votes. For k-mer counting into R using perfect hashing
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: k-mer counting into R using perfect hashing
Scholar 3.0 years ago, created an answer that has been accepted. For A: k-mer counting into R using perfect hashing

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