Search Results for "sam" - Page 2
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Showing 155 open source projects for "sam"
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Stop vibe-debugging.AppSignal's MCP server hands Claude, Cursor, or Zed your real errors, traces, and the deploy that shipped them. AI writes the fix; you review the diff.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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ASLoader
Arduino upload tool
This little Java tool allows you to upload a compiled sketch to your Arduino without using the IDE. Currently the protocols Stk500v1, Stk500v2, Avr109 and SAM-BA are implemented. That means the * Arduino Due, * Arduino Duemilanove, * Arduino Leonardo, * Arduino Leonardo ETH, * Arduino Mega, * Arduino Micro, * Arduino Nano, * Arduino Pro Mini, * Arduino Uno and maybe some others are supported. -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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Linux Engineer Toolkit Live
Portable Linux engineer toolkit for recovery, repair & data rescue
Linux Engineer Toolkit (LengToolkit) Live is a specialized, recovery-oriented Linux distribution designed for system engineers and IT professionals. Operating exclusively in Live mode, it provides a robust environment to rescue failing systems, recover lost data, and manage disk infrastructures without the need for installation. Website: https://nixovena.org/lengtoolkit -
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123FASTQ
An intuitive and efficient tool for preprocessing Illumina FASTQ reads
123FASTQ performs all the pre-processes of Illumina next-generation sequencing reads (FASTQ files) easier than ever. Download the quick user manual for the latest version: https://dl.adbioinformatics.net/NGSNeeds/myTools/123Fastq_v1.3_Manual.pdf Authors: Milad Eidi, Samaneh Abdolalizadeh, Mohammad Hossein Nassirpour Supervisors: Javad Zahiri, PhD University of California San Diego Masoud Garshasbi, PhD Tarbiat Modares University, Tehran, Iran If you use 123FASTQ,... -
AI-powered service management for IT and enterprise teamsGive your IT, operations, and business teams the ability to deliver exceptional services—without the complexity. Maximize operational efficiency with refreshingly simple, AI-powered Freshservice.
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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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Jennifer
Crystal ORM using ActiveRecord pattern with flexible query DSL
...Jennifer allows you to maintain everything for your models - from DB migrations and field mapping to callbacks and building queries. For detailed information see the docs and API documentation. For command management Jennifer uses Sam. Due to this you can easily create/migrate/drop a database or invoke a generator to bootstrap your models and migrations. Jennifer has a built-in database migration management system. Migrations allow you to organize all database changes. -
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FastQC
A quality control analysis tool for high throughput sequencing data
FastQC is a quality control analysis tool designed to spot potential problems in high throughput sequencing datasets. Its goal is to provide a simple way by which to check the quality of raw sequence data coming from high throughput sequencing pipelines. It does this by running a modular set of analyses on one or more raw sequence files in fastq or bam format. It then produces a report summarizing the results, and highlighting any areas where the library may appear unusual. This should then... -
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MOLS 2.0 is a free and open-source software package for peptide modeling and protein-ligand docking. Authors: Dr. D. Sam Paul, Dr. S. Nehru Viji, Dr. P. Arun Prasad, Dr. K. Vengadesan, Dr. N. Gautham. If you use MOLS 2.0 for publication, please cite - D. Sam Paul, N. Gautham, MOLS 2.0: software package for peptide modeling and protein–ligand docking, Journal of Molecular Modeling 22 (2016) 1–9. Publications related to MOLS 2.0: 1. Vengadesan, K. & Gautham, N. ...
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filterSAMbyVCF
his program extracts reads from SAM file according to SNPs from a VCF
filterSAMbyVCF is a Pascal command line program to separate allele-specific reads from a SAM file. This program extracts reads from SAM file according to SNPs from VCF file. Extracted reads have ALT allele at the position given in VCF file. Usage with UNIX/Linux/MacOS: ./filterSAMbyVCF vcfFile.vcf samFile.sam Usage with Windows: filterSAMbyVCF.exe vcfFile.vcf samFile.sam No warranty of any kind is provided. Use at your own risk. -
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SCVZ menza
App za prikaz jelovnika u studentskoj menzi u Varaždinu
Aplikacija napravljena u Flutter framework-u. Projekt koji sam radio u slobodno vrijeme i želim predstaviti prilikom prijave za studentsku praksu. Aplikacija komunicira s Flask serverom koji scrape-a podatke sa službene stranice menze. Server aplikaciji vraća json u kojoj se nalazi današnji jelovnik. Trenutno je server hostan na Heroku platformi. https://scvzmenza-app.herokuapp.com/danas -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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PDFsam Portable
Split, merge, extract pages, mix and rotate PDF files.
...It has all the same features as PDFsam Basic, plus, it leaves no personal information behind on the machine you run it on, so you can take it with you wherever you go. The ‘sam’ part of PDFsam's name means ‘split and merge’, and this is a large part of what the tool is designed to do. As well as making it possible to merge multiple PDFs into a single file, PDFsam Basic offers you no fewer than three ways to split PDFs. You can split using page numbers as a marker, using bookmarks contained within a PDF file, or into chunks of a particular size. ... -
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SAM Linux Portable
A portable 64bit Linux system based on Porteus Linux in EN/DE/FR/ES
additional information: Password for guest is "guest" Password for root is "toor" For now you can find more info about the possibilities at the Porteus Website: http://www.porteus.org/info/tips-and-tricks.html . -
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SAMFF
A Refined Empirical Force Field to Model Protein-SAM Interactions
...The structures and dynamics of proteins can be studied via molecular dynamics (MD) if the protein-surface interactions can be accurately modeled. Based on AMBER14 and GAFF, we systematically tuned the Lennard-Jones parameters of selected amino acid sidechains and the functional group of SAM with repeated metadynamics and umbrella sampling simulations. The final parameter set has yielded a significant improvement in the free energy values with R = 0.83 and MSE = 0.65 kcal/mol. We applied the refined force field to predict the adsorption orientation of lysozyme on CH3-SAM. For details, please refer to our publication: Bhadra and Siu, "A Refined Empirical Force Field to Model Protein-SAM Interactions Based on AMBER14 and GAFF" (submitted) https://cbbio.online/software/SAMFF/index.html -
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go-ipfs-plugin-i2p-gateway
A plugin for presenting an IPFS gateway over i2p
...It simply takes advantage of the plugin system to set up some hidden services when the IPFS plugin is initialized. It does this by reading the IPFS config file to find the ports that have been configured by the admin running IPFS, then using the SAM API to forward those ports to I2P. Once they are forwarded, a config file is generated containing the i2p configuration and it's base32 and base64 addresses. This is stored in a file called "i2pconfig." Finally, it simply forwards the IPFS gateway to I2P. -
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CONDEL is a method for detecting CNVs and deletion types from single samples using high-throughput sequence data. It can be used for analyzing genomes from tumor cells or normal cells with an input of genome reference, reference index, SAM file, and read counts.
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PySptools
Hyperspectral algorithms for Python
...New for v0.14.x: a scikit-learn bridge (alpha and partial). The functions and classes are organized by topics: * abundance maps: FCLS, NNLS, UCLS * classification: AbundanceClassification, NormXCorr, KMeans SAM, SID, SVC * detection: ACE, CEM, GLRT, MatchedFilter, OSP * distance: chebychev, NormXCorr, SAM, SID * endmembers extraction: ATGP, FIPPI, NFINDR, PPI * material count: HfcVd, HySime * noise: Savitzky Golay, MNF, whiten * sigproc: bilateral * sklearn: HyperEstimatorCrossVal, HyperSVC and others * spectro: convex hull quotient, features extraction (tetracorder style), USGS06 lib interface * util: load_ENVI_file, load_ENVI_spec_lib, corr, cov and others The library do an extensive use of the numpy numeric library and can achieve good speed. ... -
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CoVaMa
Co-Variation Mapper
CoVaMa (Co-Variation Mapper) (python) detects correlated patterns of mutations in a viral quasi-species. CoVaMa takes NGS alignment data (SAM) and populates large matrices of contingency tables that correspond to every possible pairwise interaction of nucleotides or amino acids in the viral genome. These tables are then analysed for evidence linkage disequilibrium. CoVaMa requires python version 2.7 and Numpy. -
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an implementation of the Inflate decompression algorithm corresponding to deflate compression as used by gzip and compatible with RFC 1951 Written in Z80 assembly language, with memory paging support for the Sam Coupe
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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together... -
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ophcrack
A Windows password cracker based on rainbow tables
Ophcrack is a Windows password cracker based on a time-memory trade-off using rainbow tables. This is a new variant of Hellman's original trade-off, with better performance. It recovers 99.9% of alphanumeric passwords in seconds. -
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ScummVM
A cross-platform interpreter for many point-and-click adventure games
ScummVM is a cross-platform interpreter for many point-and-click adventure games. This includes LucasArts SCUMM games (such as Monkey Island 1-3, Day of the Tentacle, Sam & Max, ...), many of Sierra's AGI and SCI games (such as King's Quest 1-6, Space Quest 1-5, ...), Discworld 1 and 2, Simon the Sorcerer 1 and 2, Beneath A Steel Sky, Lure of the Temptress, Broken Sword 1 and 2, Flight of the Amazon Queen, Gobliiins 1-3, The Legend of Kyrandia 1-3, many of Humongous Entertainment's children's SCUMM games (including Freddi Fish and Putt Putt games) and many more. ...
