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8 months ago
I am using seaborn to make a heatmap plot of 16S rDNA gene readings. I generate a heat map; however, the values in the map do not match my data.& ...

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12 months ago
Hi, . i am new to bigdata and R programming (Data science)i have doubt when i try to read a file from hdfs i.e like from sparkR(R programming) to ...

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1 year ago
This is one of the standard library utilities that is not given the attention it deserves. cgitb gives you detailed information about an error, and I ...

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1 year ago
Every time I write something in python, I like to make it possible to people to get informative message when they fail to run a tool because they are ...

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1 year ago
This is another example of plotting figures in R at CodersCrowd. As our codes are all running in containers and as we are not forcing the display ...

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1 year ago
This is an example running a linear regression within a container. We use an example published in scikit-learn website ...

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2 years ago
i dont view what is the fail ...

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2 years ago
This code doesn't work looks like some issue in defining the list in KEYS.Although all the values are mentioned properly still while executing the sys ...

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2 years ago
This is an example of bypassing the built in function in python to allow duplicate keys in python ...

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2 years ago
def check_Tm(seq):    at = seq.count("A")+ seq.count("T")    gc = seq.count("G")+ seq.count("C")    tm = ((at*2)+(gc*4)) ...

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2 years ago
This is a fancy way of getting file size in human readable format. Ok ! You can use the <code>du -h</code> command you would say ! Sure bu ...

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2 years ago
This is an example where we can use ruffus proxy logging to share the log between different tasks. Of course we can use the traditional logging stuff ...

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2 years ago
This is a quick way of displaying the git log as a nice tree on the browser.I will be cloning the google genomics repo on github as an exampleLogin to ...

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2 years ago
This is a small tool I added lately on github. I had to monitor some disk usage for our group members on our servers so I had to develop a small cron ...

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2 years ago
Test Programs ...

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2 years ago
A function to shuffle multiple NumPy arrays in unison. One typical use case could be the shuffling of training data and the corresponding class labels ...

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2 years ago
This is a small function that I am using in one of my pipelines that send information about the size of a specific file, It is fun to use and may be u ...

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2 years ago
Given a list of number pairs, where each number in the pair is separated by a space as in "a b". Where 0 < a < b <= 10000 ...

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2 years ago
A small reminder on how to do that in ruffus, pretty straightforward  ...

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2 years ago
A small function to plot the decision regions of machine learning classifiers. ...

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2 years ago
i don't know why its not working ...

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2 years ago
I just struggled a little bit of converting ~10 Gb sized CSVs to SQLite databases for more effective processing because of memory issues :PI came up w ...

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2 years ago
A customer in a store is purchasing five items. Design a program that asks for theprice of each item, and then displays the subtotal of the sale, the ...

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2 years ago
Find errors ...

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2 years ago
Very new to coding not sure if my strings are right can I get some help?   I am trying to have a name, gender,food, and dog.   ...

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2 years ago
I came across this nice package python-progressbar and I am sharing one of the examples they provide. It is a nice way of keeping your package users a ...

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2 years ago
Help me find the errors in that code as I failed to execute them in python 2.7.2 ...

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2 years ago
I am heavily into sports predictions these days where I collect raw data from various different sources. One of the challenges is to merge the informa ...

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2 years ago
The shell commands like `find` inlinux/unix environments are quite powerful and useful. However, often I want to get a bunch of file paths as an itera ...

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2 years ago
Hi,I was recently competing in several kaggle competitions and implemented a weighted majority-rule EnsembleClassifier. The idea is to combine se ...

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2 years ago
I found this package useful in case we want to display nice tables as output in some python programs, so I tried it and decided to add it to CodersCro ...

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2 years ago
This is a small task that we may do frequently, given a regions list we would like, for each region, get the nearest flanking gene, although the ...

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2 years ago
This script finds the multiplies of 3 and 5 merge the two list into one excluding the duplication and calculates the summary of their values. ...

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2 years ago
''' The circumstances ''' def bemoan(): print('Alas!') our_lives_must = ['end'] the_suffering = [True] # Read as "the suff'ring" she = ...

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3 years ago
this is one of the snippets I have configured with my Sublime Editor, I like to have some snippets and code like that to play with the data or if I ha ...

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3 years ago
This pipeline was designed and written in Perl by Severin Zinöcker and Michael Waisberg at National Institutes of Health in 2013 and 2014.The pu ...

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3 years ago
This pipeline was designed and written in Perl by Severin Zinöcker and Michael Waisberg at National Institutes of Health in 2013 and 2014.The pu ...

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3 years ago
This pipeline was designed and written in Perl by Severin Zinöcker and Michael Waisberg at National Institutes of Health in 2013 and 2014.The pu ...

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3 years ago
This is a runnable version of the great learnxinyminutes series focused on python. I adapted the course at this page http://learnxinyminutes.com/ ...

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3 years ago
I am a novice programmer. I made this script to search for DNA Fur-binding sequences (ATTATTANTAATAAT or TAATAATNATTATTA), allowing for up to 2 mismat ...

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3 years ago
There is a lot of tools out there, very useful for command line usage, and very widely used in Bioinformatics, which rapidly turns out to be annoying ...

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3 years ago
Programme de réencodage de vidéo ...

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3 years ago
Hi, I'm trying to generalize my program for a planetary orbit to more planets, so I wrote a Planet class.I know it works because it prints the positio ...

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3 years ago
This is a Bayesian classifier that handles conditional dependence by splitting the feature space into pairs and approximating the cummulative probabil ...

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3 years ago
I came across this package lately and I decided to test it since I was always looking at an ORM like system but with no database layer related to it, ...

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3 years ago
This is a quite usual task we always run through, we have a target (region) list with location and we want to get the coverage from a bam file on thes ...

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3 years ago
The code opens a miRNA fasta file and removes the redundant miRNA sequences by using hashes. ...

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3 years ago
This code opens a sif (network) file and as output gives numbers for each number of FFLs.  ...

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3 years ago
The code here tries to open a fasta file including mature miRNA sequences and read them for counting their 3mer contents. Here the purpose is to show ...

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3 years ago
[edited by moderators] please add the code in the section reserved to in the future, thanks ...

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3 years ago
Reading and Writing fastq compressed files is done frequently in NGS analysis. The below code helps to handle both the fastq compressed/uncompres ...

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3 years ago
In this code I am parsing a fastq file and I am extracting all sequences length to an array, that I feed to numpy and then got the average sequence le ...

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3 years ago
I am working on a pipeline with Ruffus and I have a lot of Tasks that depends on other Tasks using the @follows decorator. It happens that when testin ...

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3 years ago
One of the usual tasks when it comes to examine an alignment file is to check the number of reads that successfully mapped to the reference genome and ...

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3 years ago
Django middleware that can turn any url of your application into its own profile, either as text output or as binary output that can later be analysed ...

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3 years ago
I came through this approach to intersect dataframes in R, I am sure there is a lot of other way of doing this but this solved my problem today :), if ...

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3 years ago
I am developing a pipeline, and the program is outputting a lot of information in stderr that I didnt want to store in log file, I just need one or tw ...

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3 years ago
I have a large tabular blast file that I am trying to filter.I would like to print the first instance of a match, and the any reflections of a match.F ...

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3 years ago
I added Ruffus as a runnable instalnce at CodersCrowd in order to showcase all good things that can be built with this library, and also to solve prob ...

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3 years ago
Today I wanted to monitor a code block in python and I was interested in knowing basic information on elapsed time per function. A lot of solutions ex ...

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3 years ago
I am using the default color palette from ggplot2 and would like to be abe to extract the colors mapped to my variablemy function is like follows :p = ...

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3 years ago
Function to read a fasta file.  Yields id, sequence pairs.  Its a generator so sequences can be read into memory and discarded, or stored in ...

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3 years ago
Hi,This is a particular question. As you all know we are making it possible to run codes @CodersCrowd, what a lot of members suggested is that most co ...

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3 years ago
Here is an example of something I wanted to be implemented directly in intersectBed that can sometimes be useful. It would be great to adda flavor of ...

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3 years ago
Another implementation of SW algorithm. This example can be used and embedded into a code that relies on SW for local alignment, I find it handy for e ...

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3 years ago
Here is something I do frequently, I just thought it might be useful to share. Sometimes I do create dataframe and do some graphic output using ggplot ...

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3 years ago
A lot of big streaming companies like Spotify, Pandora, etc are more and more pushing towards a better and more stable frameworks and the best thing t ...

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3 years ago
Hello all,I am using a pachage from Bioconductor TEQC, and when I load my reads as a bam file, the object created (class RangedData) looks like thisRa ...

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3 years ago
Here is a one useful awk line to extract a column from a list of files and create a tabular file out of them.Very easy and very fastRad ...

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3 years ago
This is an example of a task I had to do and I opted for using awk. I had to do that for custom local alignment of these end of reads. The script ...

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3 years ago
As any process that you would run on python, I used to use subprocess on my python codes to run bedtools utilities such as intersectBed, until I met p ...

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3 years ago
As I am sure many of you, I use extensively join, sort and grep programs in the shell.However, although very fast, these programs do have some limitat ...

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3 years ago
Hello, I am trying to use this code to extract sequence in Fasta format from Genbank but I am getting an error on a variable not known, can someo ...

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3 years ago
Here is an implementation (one of many on the web), of the local and global alignment in python. I am creating this code with errors introduced intent ...

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3 years ago
Today I used ShortRead R package when I was checking a series of fastq files after finding out that I had an alignment showing huge coverage at some p ...

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3 years ago
This is a small awk script to find records of one file in a second file. The records are matched via a common field. ...

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4 years ago
The ChipBase contain already processed Chip-Seq peaks, so sometimes one wants to directly use their result without the need to go  thro ...

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4 years ago
Using a for loop it counts all reads contain in every BAM file.Ouput: Filename and Total Number of Reads ...

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4 years ago
This is a small python script to convert csv files into xlsx files.It is nothing fancy. Nevertheless, it comes in handy when you are working with ...

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4 years ago
A script for gene set enrichment over KEGG, the perl script serves as automation for the analysis of several gene set files inside a directory, the R ...

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4 years ago
The python script rpkmforgenes.py is written for calculating gene expression for RNA-Seq data. It was used for a study published in PLoS Computational ...

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4 years ago
I normally work in Make but would like to transition to Ruffus or bpipe.If you are familiar with either of these pipeline platforms please g ...

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4 years ago
A basic example script using the Biomart Rubygem to retrieve genomic co-ordinates based on a text list of reference transcript ids. Used to construct ...

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4 years ago
GATKs "CombineVariants" pretty effectively merges VCFs over even thousands of samples. Unfortunately, it is unable to also merge some of the less ...

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4 years ago
I am trying to extract flanking regions of a list of SNPs, I implemented my code in R using Bioconductor and even though the process seems straightfor ...

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4 years ago
CIGAR strings are a mandatory field in the Sequence Alignment/Mapping (SAM) specification. This field describes the relationship between the alignment ...

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4 years ago
This is a part 3/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...

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4 years ago
This is a part 2/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...

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4 years ago
This is a part 1/3 of "one-line series". One-line commands with perl, awk or sed are very useful in bioinformatics for data/files manipulation. There ...

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4 years ago
This is an interesting implementation for RNA-seq analysis in python developed by Hanfei Sun. You can find the source code and the documentation https ...

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4 years ago
This script calls the program bigWigSummary to extract enrichment from a bunch of bigWig files (they can be a lot of ChIP-seq experiments for example) ...

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4 years ago
This program reads a bowtie alignment file and writes  an output file with the informations about the chromosome, the position the strand of the ...

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4 years ago
Groovy code to run a cypher graph query on a neo4j instance.  This uses the REST endpoint of the server so there are no neo4j libraries needed an ...

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4 years ago
Hello I am trying to use sed to reformat a file, specifically remove new lines (\n) and replace them by spaces to previous linesmy original file ...

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4 years ago
Obtaining the actual sequence making up a gene from NCBI is simple using a browser, but not so much when wanting to do it in batch. This script obtain ...

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4 years ago
A sample script using the ETE package to detect shift in internal nodes where a significant change in enrichment values (could be anything) happens ...

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4 years ago
Multifasta Parser is a new parser for fasta files. basically allows you to extract fasta sequences from multifasta file. ...

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4 years ago
A typical task in bioinformatics analysis is the usage of online tools. Regardless of the task to be done, there is a general approach to display resu ...

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4 years ago
Analyze human Genome in R. Read more here http://www.biocodershub.net/community/analyzing-human-genome-r-scripts/ and here http://userwww.service.emor ...

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4 years ago
Homemade Genbank report parser using regular expressions. Once desired data is captured, it can be printed in any format.WI Bioinformatics course - Fe ...

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4 years ago
Correlation is one of the most used tasks in computational biology, while using packages like R is very simple, sometimes we need to do it on the fly ...

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4 years ago
This is one of many methods to parse Blast output, written in perl. See comments in the script for usage ...

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