Search Results for "reference"
Sort By:
Showing 75 open source projects for "reference"
View related business solutions-
Build Secure Enterprise Apps Fast with RetoolCreate internal software that meets enterprise security standards. Retool connects to your business data—databases, APIs, and vector stores while ensuring compliance with granular permissions and audit logs. Whether on our cloud or self-hosted, build the dashboards and admin panels your organization needs without compromising on security or control.
-
Find Hidden Risks in Windows Task SchedulerWindows Task Scheduler might be hiding critical failures. Download the free JAMS diagnostic tool to uncover problems before they impact production—get a color-coded risk report with clear remediation steps in minutes.
-
1
Sherloq
An open source digital image forensic toolset
Sherloq is a research-oriented toolkit designed for digital image forensics, providing an integrated environment to experiment with algorithms for image analysis and tampering detection. Rather than functioning as an automated decision-making system, it serves as a companion tool for researchers, enthusiasts, and students who want to explore forensic techniques from scientific literature and workshops. The project emphasizes transparency and community collaboration, contrasting with... -
2
Perl 5
The Perl programming language
This repository contains the reference implementation of the Perl 5 programming language, including the interpreter, core modules, build system, and an extensive test suite. Perl 5 is a multi-paradigm language renowned for powerful text processing, rich regular expressions, and pragmatic glue code across systems. The core distribution is highly portable, building on Unix, Linux, Windows, and many other platforms, with stable release cycles and careful back-compatibility. -
3
Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing customizable databases so researchers can bias domain or strain-specific annotations. The pipeline is optimized for speed, using multithreading and caching to annotate large microbial genomes in minutes. ... -
4
Learning-SICP
Collection of Chinese cultural projects and course learning materials
Learning-SICP is a community project that localizes the MIT course “Structure and Interpretation of Computer Programs” (SICP) and curates complementary study materials for learners, especially Chinese-speaking Scheme/Lisp students. It focuses on translating the official lecture subtitles into Chinese while preserving the original English content for reference, providing an approachable path to a classic foundational course in computer science. The repository organizes translated subtitles, lecture indices, and supporting documents so learners can follow along with the full video series and consult the book and related readings as they study. Beyond subtitles, it aggregates links to the SICP text, environment setup guides, extended exercises, and FAQ resources to smooth first-time setup and deepen understanding of the material. -
Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
-
5
Golang Regex Tutorial
Golang - Regular Expression Tutorial
...The repository is designed to help developers understand not only the syntax but also the practical implementation of pattern matching in Go. With its structured format, it serves both as an introductory guide and as a reference for intermediate users who want to strengthen their understanding of regular expressions in Go. -
6
RefDB is a reference database and bibliography tool for SGML, XML, and LaTeX documents, sort of a Reference Manager or BibTeX for markup languages. It is portable and known to run on Linux, Free/NetBSD, OSX, Solaris, and Windows/Cygwin.
-
7
miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
...By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also markedly improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. Reference: https://doi.org/10.1093/bioinformatics/bty972 -
8
TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
9
ggplot2-book
ggplot2: elegant graphics for data analysis
...The book explains the theory and application of the ggplot2 package in R for data visualization, guiding readers through its layered grammar of graphics approach. It serves as both a practical guide and conceptual reference for building advanced plots and mastering ggplot2. -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
-
10
OpenATPOL
A reference implementation of the Polish geobotanical grid
This project is a reference, open source implementation of the coordinate conversion algorithms for the Polish geobotanical grid called ATPOL. -
11
zeroclickinfo-goodies
DuckDuckGo Instant Answers based on Perl & JavaScript
ZeroClickInfo Goodies is a collection of Perl and JavaScript-based instant answers for DuckDuckGo. It provides users with immediate answers to queries without the need to click on search results. -
12
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... -
13
BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...In default threshold 30X data (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. Google group for help: http://goo.gl/zL7Nj -
14
SIMM
SIMM: Simultaneous Identification of Multiple Mutations
SIMM (Simultaneous Identification of Multiple Mutations) pipeline provides a workflow to align the clean reads to reference genome, call SNPs between mutants and reference genome, then genotype the SNPs and identify causal mutations from different mutants simultaneously without the sequencing information of wild-type progenitor. Individuals with mutant homozygous phenotype are bulked and sequenced to >20X, and then analyzed with SIMM to identify causal mutation(s) responsible for the mutant phenotype. ... -
15
datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS... -
16
CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
...To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target sites and queries the reference genome as well as a CRISPR system with a defined spacer length and PAM sequence, this standalone tool will identify putative sites and assign a predicted activity based on support vector machine model which conducted by sgRNA Scorer 2.0. In addition, sgRNAs with minimal off-target activity were predicted by Cas-OFFinder, and score with Off-Target Cutting Frequency Determination (CFD). -
17
EQGRP
Decrypted content of eqgrp-auction-file.tar.xz
EQGRP is a public release of the so-called Equation Group hacking tools, originally leaked online in 2017. The repository serves as an archive and reference for security researchers, documenting the exploit frameworks, implants, and utilities that were allegedly used by a highly sophisticated threat actor. The tools include network exploitation scripts, backdoors, and frameworks targeting a range of platforms and services, many of which highlight previously unknown vulnerabilities. ... -
18
Xcode Shell
shell script that used to auto-build xcode project
...These scripts are designed for macOS environments with Xcode command line tools installed and rely on simple configuration for server publishing or email notifications. While no longer actively maintained, xcode_shell remains a practical reference for lightweight automation of iOS app build and distribution processes. -
19
Kinannote
Protein Kinase Identification and Classification
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes. Kinannote runs on a unix command line and depends on local hmmer 2 and Blast 2.24 installations. Citing Kinannote: Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily Jonathan M. Goldberg; Allison Griggs; Janet L. Smith; Brian Haas; Jennifer Wortman; Qiandong Zeng Bioinformatics 2013; doi: 10.1093/bioinformatics/btt419 http: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full pdf: http://bioinformatics.oxfordjournals.org/content/29/19/2387.full.pdf+html -
20
RGAAT
Reference based genome assembly and annotation for new genome
This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format). -
21
CNVision
CNV prediction from Illumina genotyping data
...CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision: http://www.ncbi.nlm.nih.gov/pubmed/21658581 -
22
Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. -
23
MPPerl::Convert::ASCII85::XS
Convert to/from ASCII base-85 encoded text
This module provides functions for conversion between binary data and ASCII base-85 encoded text as described by Adobe in the PostScript Language Reference. There is also a non‐standard mode that encodes a group of four consecutive ASCII SPACE characters as a single ‘y’ character, and omits the ‘~>’ EOD marker. -
24
ASCII85-Tools
Convert between binary data and ASCII base-85 encoded text
This package consists of two command-line utilities and an accompanying Perl module that let you convert between binary data and ASCII base-85 encoded text as specified by Adobe in the PostScript Language Reference. There is also a C version available; please see the C/ directory in the Files section. -
25
MPPerl::Convert::ASCII85
Convert to/from ASCII base-85 encoded text
This module provides functions for conversion between binary data and ASCII base-85 encoded text as described by Adobe in the PostScript Language Reference. There is also a non‐standard mode that encodes a group of four consecutive ASCII SPACE characters as a single ‘y’ character, and omits the ‘~>’ EOD marker. Please note that this module is written in pure Perl, and is as such very slow. A better alternative is to use the MPPerl::Convert::ASCII85::XS module, in which the most time-critical code has been written in C. ...
