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samtools

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  Analyzed 5 months ago

SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAM tools provide efficient utilities on manipulating alignments in the SAM format.

25.7K lines of code

14 current contributors

5 months since last commit

4 users on Open Hub

Activity Not Available
0.0
 
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picard

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  Analyzed 8 months ago

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.sourceforge.net) format.

77.6K lines of code

0 current contributors

almost 3 years since last commit

2 users on Open Hub

Activity Not Available
5.0
 
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Licenses: No declared licenses

pysam

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  Analyzed 14 days ago

Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

132K lines of code

18 current contributors

about 1 month since last commit

2 users on Open Hub

Moderate Activity
4.0
   
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Exome Variant Analysis

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  Analyzed 5 months ago

Exome Variant Analysis Pipeline (NGS Data). Developed in R language, calling external programs for specific tasks. It can be run in parallel using many processors from the same machine, and can be easily extended to run in computer clusters (HPC). Still in its early stages, it's a work in progress ... [More] that is being used already for production in some research centers. Features: * Quality Control * Mapping in a reference genome * Tasks related to variants: ** Calling ** Filtering ** Annotating ** Reporting effects and basic statistics * Sending an email once the run is finished. More information: ueb(a)vhir.org [Less]

2.31K lines of code

0 current contributors

almost 4 years since last commit

1 users on Open Hub

Activity Not Available
5.0
 
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Licenses: CC-BY-SA-3.0, LGPL-3.0+

Collagene

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  Analyzed 5 months ago

Software for cloning

13.5K lines of code

0 current contributors

almost 2 years since last commit

1 users on Open Hub

Activity Not Available
0.0
 
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bio-bwa

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  Analyzed 5 months ago

14.8K lines of code

6 current contributors

10 months since last commit

1 users on Open Hub

Activity Not Available
0.0
 
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Molecular Genetics Information System

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  No analysis available

This project is aimed at developing an open source information system for an efficient management of data deriving from Sanger sequencing and microsatellite genotyping experiments.

0 lines of code

0 current contributors

0 since last commit

0 users on Open Hub

Activity Not Available
0.0
 
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Mostly written in language not available
Licenses: No declared licenses

btween

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  Analyzed 11 months ago

Important note: development (if any) is now focused on hxMotion branch. It currently compiles to Javascript and Haxe>SWF9, and once it's more complete I'll keep an updated SWC export for use with AS3. It's neat to use it with haxe, though, I love the syntactic sugar that 'using' keyword allows ... [More] for, such as: ball.tween({x:200}).start.queue().back(); This project is in public repository since Sep 2008. It's been created in the first half of 2007, while flex sdk was still in beta. First deployed project using it was an interface for BBC Scottland, dating back to July 2007. So don't dare calling this 'new', please. "If God does not exist, everything is permitted" - Fyodor Dostoevsky, in The Brothers Karamazov "'Everything is permitted' does not mean that nothing is forbidden..." / "One can be virtuous through a whim" - Albert Camus, in The Absurd Man BTween is aimed to provide both a very strict and verbose syntax - which motivated me to write this api - and a very loose, quick'n'dirty one. First one is intended to comply with the complexity of current flash/flex applications, which will benefit from the tighter use of good OOP practices and patterns. Second is given to the simple uses we still may have of flash - you certainly won't want to loose time creating a fully standardized and documented application when coding a simple banner, for example. I strongly disrecommend the use of long chains of tweens in a single line for a serious application, as well as I recommend the use of the regular Event model in most cases, and the instantiation of BTween objects instead of the "static calls" way. So this looks good to me: var tween:BTween = new BTween(); tween.queue(trace,"I'm a callback"); tween.add({target:blueBall,y:100}); tween.add({target:redBall,y:200}); tween.start();While this might be good for a banner that will be sent to trash after a couple of days of use BTween.make().start({target:blueball,y:10},{target:redBall,y:200}).queue(doSomething);With this being an intermediary approach: var tween:BTween = new BTween(); tween.queue(doSomething); tween.start({target:blueball,y:10},{target:redBall,y:200});This flexibility haven't made of BTween a sumo fighter, though. The minimal footprint is around 3k, making it light enough to be used in banners or other weight-sensitive uses. The API is also meant to be easily extensible, you can actually code your own extension in a few minutes, implementing IProperty or ISequenceable interfaces. BTween is in ALPHA state, though I've been using it for almost an year, and even its design is being improved each day. If anyone is interested in helping, I'd be happy to give commit rights. Just contact me. Please send your thoughts to pedromoraes@gmail.com. No beginner support requests please. [Less]

8.06K lines of code

0 current contributors

almost 6 years since last commit

0 users on Open Hub

Activity Not Available
0.0
 
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seqtoolbox

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  Analyzed 11 months ago

Analysis of gene expression, ChIP-seq and CNA data generated using massively parallel sequencing data

0 lines of code

0 current contributors

almost 8 years since last commit

0 users on Open Hub

Activity Not Available
0.0
 
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Mostly written in language not available
Licenses: MIT

atlas-cnv

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  Analyzed over 5 years ago

Detect Copy Number Variations from high-throughput genome sequencing.

5.15K lines of code

0 current contributors

almost 8 years since last commit

0 users on Open Hub

Activity Not Available
0.0
 
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