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Showing 16 open source projects for "run sackboy run"
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. ... -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis... -
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crossmap
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format. -
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the... -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
...The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc. - to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes. -
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RELEASE NOTE: Get raxmlGUI 2.0 at the NEW PROJECT LOCATION: https://antonellilab.github.io/raxmlGUI/ raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used software for phylogenetic inference using maximum likelihood. A userfriendly graphical front-end for phylogenetic analyses using RAxML (Stamatakis, 2006). Please cite: Silvestro, Michalak (2012) - raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12, 335-337. DOI:...
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
...SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use. -
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
...It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. https://cbbio.online/software/protpos/ -
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This script can convert raw diffraction images to JPEG files. Support ADSC, MarCCD, Mar345, RAXIS and PILATUS, and can be run on Windows, Linux and Mac OS X.
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a... -
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
BiSA is a bioinformatics database resource that allows investigators to run a number of overlapping genomic region analyses using their own datasets, or against the pre-loaded Knowledge Base. Analysis results can be restricted to a chromosome; the minimum base pair overlap in two sets or maximum distance between regions can be set; as can the maximum allowed distance between region centres. BiSA is capable of reporting overlapping regions that share common base pairs; regions that are nearby; regions that are not overlapping; average region sizes. ... -
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QUASR
Cross-platform NGS processing and analysis pipeline in Python
...Functions include: duplicate removal demultiplexing primer-removal quality-assurance (QA) graphing quality control (QC) consensus-generation minority-variant determination minority-variant graphing The main current version is 6.X, which is written in Python3. 7.X is my rewrite in Java, but is still work in progress. Both are written to be as lightweight as possible so they can run with minimal memory-requirements on a desktop or laptop as well as on a compute cluster. If you have any problems with QUASR, please do contact me at the email address provided in the README. -
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Atlas2Cloud
Atlas2 Genome Analysis Pipeline on Amazon Web Services
...Alternatively, the code can also be used for running the pipeline from your computer. By installing this software on your computer you will be setting up your computer to act as the head node which would then run the pipeline from your computer. -
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...Amplicon is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac
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jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
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..., for "Hordes of Little Atoms," is a project to develop a lean, modular, scalable toolkit for massive simulations of particle (molecular) dynamics. It is written in C and Python to get the best balance between programmer and run time.
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