Search Results for "seq"
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Showing 177 open source projects for "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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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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Bowtie 2
A fast and sensitive gapped read aligner
...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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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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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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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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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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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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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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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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Iperf 2
A means to measure network responsiveness and throughput
Iperf here is a means of measuring networks - capacity & latency (including ECN) over sockets both TCP and UDP. The goals include maintaining an active iperf code base across a broad set of platforms and operating systems. This is a multi-threaded design that scales with the number of CPUs or cores within a system. It supports both high impact and low impact techniques to obtain and report network performance. Current release: 2.2.1, Nov 4th, 2024 About iperf 2 and iperf3: Read... -
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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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CPAT
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). ... -
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FastQC
A quality control analysis tool for high throughput sequencing data
...This should then direct you to where your data may have problems and allow you to take necessary steps to correct it before doing any further analysis. FastQC is not tied to any specific type of sequencing technique, so it can be used to look at libraries of various experiment types (Genomic Sequencing, ChIP-Seq, RNA-Seq, BS-Seq etc etc). -
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CPT
CPT: A Pre-Trained Unbalanced Transformer
...Token embeddings found in the old checkpoints are copied. And other newly added parameters are randomly initialized. We further train the new CPT & Chinese BART 50K steps with batch size 2048, max-seq-length 1024, peak learning rate 2e-5, and warmup ratio 0.1. Aiming to unify both NLU and NLG tasks, We propose a novel Chinese Pre-trained Un-balanced Transformer (CPT). -
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OmicSelector
Feature selection and deep learning modeling for omic biomarker study
OmicSelector is an environment, Docker-based web application, and R package for biomarker signature selection (feature selection) from high-throughput experiments and others. It was initially developed for miRNA-seq (small RNA, smRNA-seq; hence the name was miRNAselector), RNA-seq and qPCR, but can be applied for every problem where numeric features should be selected to counteract overfitting of the models. Using our tool, you can choose features, like miRNAs, with the most significant diagnostic potential (based on the results of miRNA-seq, for validation in qPCR experiments). -
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Cyclops
An advanced platform for writing functional applications in Java 8
Fast purely functional datastructures (Vector, Seq / List, LazySeq / LazyList, NonEmptyList, HashSet, TreeSet, TrieSet, HashMap, LinkedMap, MultiMap, TreeMap, BankersQueue, LazyString, Discrete Interval Encoded Tree, Zipper, Range, Tree, DifferenceList, HList, Dependent Map). Structural Pattern Matching API (deconstruct algebraic product and sum types). Improved type safety via the removal of unsafe APIs -- E.g. -
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CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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CSReadGen
RNA-Seq read simulator that offers a wide range of parameter options.
> CSReadGen wiki: https://sourceforge.net/p/csreadgen/wiki/Home/ Related software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: (See wiki) 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ 6. SeQuester: https://sourceforge.net/projects/sequester/ 7. TreeScope: https://sourceforge.net/projects/treescope/ -
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scDAPA
Detection and visualization of dynamic alternative polyadenylation
scDAPA - a tool for detection and visualization of dynamic alternative polyadenylation from scRNA-seq data [1] scDAPA user manual Please visit the Wiki page of this website. [2] scDAPA Q&A For Q&A, please visit the Blog page of this website. [3] scDAPA bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite scDAPA? Ye C, Zhou Q, Wu X, Yu C, Saban D.R, Li Q.Q (2020) scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. ...
