Search Results for "rna-seq"
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Showing 420 open source projects for "rna-seq"
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. ... -
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to address the statistical challenges of single cell RNA-seq. ... -
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RSeQC
RNA-seq data QC
RSeQC provides a number of functions to evaluate the quality of RNA-seq data. http://rseqc.sourceforge.net/ -
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ShowEQ or SEQ for short is a program designed to decode the EverQuest data stream and display that information on another computer running the Linux OS in real time. Our Forums are located at https://seq.sourceforge.net/forums/
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Bowtie 2
A fast and sensitive gapped read aligner
...The tool builds compact FM-index-based reference indexes, keeping memory usage low even for large genomes like the human genome. Bowtie 2 outputs alignments in SAM format and includes companion utilities for building and inspecting indexes. It is widely used in bioinformatics pipelines for RNA-seq, DNA-seq, metagenomics, variant analysis, and other sequencing-based research tasks. Overall, Bowtie 2 remains a foundational command-line tool for high-throughput sequence alignment and reproducible computational biology workflows. -
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harmonypy
Integrate multiple high-dimensional datasets with fuzzy k-means
...Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. -
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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published in the following paper: Yang Liao, Gordon K Smyth and Wei Shi. "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote", Nucleic Acids Research, 2013, 41(10):e108 -
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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This Shiny app provides a user-friendly interface for performing Weighted Gene Co-expression Network Analysis (WGCNA) on RNA-seq/Microarray and DNA methylation (Array/Sequencing) data. It allows for data upload, parameter customization, visualization of results, and exporting of analysis outputs. Online webserver https://shinywgcna.serve.scilifelab.se/app/shinywgcna PLEASE NOTE Datasets with larger dimensions (e.g., 1000x100) may fail on the server,because it is only running on 1GB RAM allocation. ...
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Immutable.js
Immutable collections for JavaScript
Immutable.js offers a collection of Persistent Immutable data structures for JavaScript. Immutable data is unchangeable once created, which makes application development so much simpler. There’s no defensive copying, and you get advanced memoization and change detection techniques with simple logic. Persistent data gives you a mutative API, one that doesn’t update data in-place but always produces new and updated data. The data structures that Immutable.js provides include List, Stack,... -
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Nethermind
A robust execution client for Ethereum node operators.
Nethermind is a high-performance, highly configurable Ethereum execution client built on .NET and designed for professional node operators. It provides fast synchronization, reliable JSON-RPC access, and support for major consensus mechanisms including PoS, Ethash, Clique, and AuRa. With features like Grafana dashboards and enterprise-grade logging, Nethermind makes monitoring and maintaining healthy nodes straightforward. Its architecture emphasizes speed and resilience, synchronizing to... -
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rna-test
script for variant calling of RNA-Seq
rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. Disable BQSR (-skb) opteion is added. New avsnp(150) is updated. use -dcov in SplitNCigarReads... -
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Rust Latam
Learn to write Rust procedural macros
This is a workshop/repository by the Rust developer David Tolnay (dtolnay) intended to teach how to write Rust procedural macros (derive macros, function-like macros, attribute macros). The repo contains multiple toy/realistic macro projects drawn from real use-cases: e.g., derive(Builder), derive(CustomDebug), seq!, #[sorted], #[bitfield]. The README indicates the focus is on learning: parsing token streams, generating code, handling generics, attribute arguments, etc. It has test harness and workflow guidance. Because procedural macros are quite subtle in Rust, this workshop is a strong resource for anyone wanting to go from beginner to intermediate/advanced macro writing. -
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Cheshire
Clojure JSON and JSON SMILE (binary json format) encoding/decoding
Cheshire is a high-performance JSON encoding and decoding library for Clojure, built atop Jackson to combine fast parsing/generation with advanced support for types like Dates, UUIDs, Sets, Symbols, and the binary JSON SMILE format. Custom encoding is supported from 2.0.0 and up if you encounter a bug, please open a GitHub issue. From 5.0.0 onwards, custom encoding has been moved to be part of the core namespace (not requiring a namespace change). Custom and Core encoding have been combined... -
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CTK
CLIP Tool Kit (CTK)
CTK (CLIP Tool Kit) is a computational biology toolkit implemented in Perl, designed for analyzing CLIP sequencing data. It offers a streamlined pipeline from raw reads through peak calling and motif discovery. -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
...It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. ... -
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IsoQuant
Transcript discovery and quantification with long RNA reads
IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ... -
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ruamel.yaml
ruamel.yaml is a YAML 1.2 parser/emitter for Python
ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order -
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cnvkit.sh
A short script to run cnvkit
cnvkit.sh is a shell script to run CNVkit for exome-seq. The shell uses the files produced by exome_test.sh. It allows for recentering the baseline by the average log2ratio of a certain chromosome. ***Update*** The seg can be annotated by cytoband with multithreading. Individual chromosomal scattergrams are plotted. -
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hg38 version of the pipelines for whole exome sequencing: exome_test38.sh wole transcription sequencing: rna_test38.sh somatic calling: somatic38.sh SV detect: svdetect38.sh, meerkat38.sh cnv: svdetectcnv38.sh, contra38.sh, cnvkit38.sh *** Mutect2 instead of haptotypecaller is used to call variants in DNA-seq.
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...It provides an object-oriented, free-software and cross-platform package for editing and playing music, importing and exporting data using various formats. It is a copy of the chord-seq object of OpenMusic, with a "in-field" quantitation system and exports to xmlMusic,
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UniversalMer2
A CLI k-mer counting tool for multiple size of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). This kmax can be specified as any length or can be automatically determined by the longest repeated patterns found in the input sequence. -
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oxDNA
A code primarily aimed at DNA and RNA coarse-grained simulations
The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases. -
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UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.