Topic: genome-analysis Goto Github
Some thing interesting about genome-analysis
Some thing interesting about genome-analysis
genome-analysis,Viral genome assemble and characterisation
User: agudeloromero
genome-analysis,Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Organization: ampliconsuite
genome-analysis,Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
User: asntech
Home Page: http://intervene.rtfd.io/
genome-analysis,Unique sequence search by K-mer exclusion
User: berybox
genome-analysis,[in development] Proof-of-Concept variation translation, validation, and registration service
Organization: biocommons
Home Page: https://github.com/biocommons/anyvar
genome-analysis,non-redundant, compressed, journalled, file-based storage for biological sequences
Organization: biocommons
genome-analysis,provides common tools and lookup tables used primarily by the hgvs and uta packages
Organization: biocommons
genome-analysis,Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Organization: biocommons
Home Page: https://hgvs.readthedocs.io/
genome-analysis,Statistical and computational analysis of the human genome
User: boulderrinnlab
genome-analysis,A minimal genetic data explorer that processes all genetic information locally.
User: brandonsaldan
Home Page: https://codex-brandonsaldan.vercel.app/
genome-analysis,visual analysis of your VCF files
User: cccnrc
genome-analysis,BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
Organization: cmu-safari
genome-analysis,Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).
Organization: cmu-safari
genome-analysis,The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957
Organization: cmu-safari
genome-analysis,RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)
Organization: cmu-safari
Home Page: https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440
genome-analysis,Tutorials for the crisprVerse
Organization: crisprverse
genome-analysis,Simple and fast html5 canvas based genome browser
User: dbkero
Home Page: http://kero.hgc.jp/
genome-analysis,Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
User: fjdf
genome-analysis,Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
User: fmalmeida
Home Page: https://bacannot.readthedocs.io/en/latest/
genome-analysis,Long-reads Gap-free Chromosome-scale Assembler
Organization: ganlab
genome-analysis,A collaborative notebook for genes and genomes
Organization: genenotebook
Home Page: http://genenotebook.github.io/
genome-analysis,Using combined evidence from replicates to evaluate ChIP-seq peaks
Organization: genometric
Home Page: https://genometric.github.io/MSPC/
genome-analysis,Archived code for analyses in "Extensive phylogenomic discordance and the complex evolutionary history of the Neotropical cat genus Leopardus" (Lescroart et al. 2023, MBE)
User: jlescroart
genome-analysis,PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features
User: kiranjavkar
genome-analysis,H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
User: kishwarshafin
genome-analysis,Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
Organization: laborberlin
genome-analysis,A random forest classifier to identify contigs of plasmid origin in contig and scaffold genomes
User: leaemiliepradier
genome-analysis,zgtools-pipeline: A pipeline that allows for the convenient acquisition of T2T (Telomere-to-Telomere) genomes.
User: linyuiz
Home Page: https://github.com/linyuiz/zgtools-pipeline
genome-analysis,Bioinformatics on GCP, AWS or Azure
User: lynnlangit
genome-analysis,[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
Organization: magics-lab
genome-analysis,Randomly subsample sequencing reads or alignments
User: mbhall88
Home Page: https://doi.org/10.21105/joss.03941
genome-analysis,De novo genome assembly and multisample variant calling
Organization: mcveanlab
Home Page: https://github.com/mcveanlab/mccortex/wiki
genome-analysis,Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Organization: miraldilab
genome-analysis,A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
User: moshi4
genome-analysis,Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
Organization: nbchub
Home Page: https://github.com/NBChub/bgcflow/wiki
genome-analysis,Handy reusable bioinformatic scripts
User: pdimens
genome-analysis,An Efficient Swiss Army Knife for Population Genomic Analyses in R
User: pievos101
genome-analysis,iPat allows you to perform GWAS and GS with drags and clicks!
User: poissonfish
Home Page: http://poissonfish.github.io/iPat/
genome-analysis,A curated list (with links) of useful tools for genome-wide association analysis.
User: raydebashree
genome-analysis,metaUSAT is a data-adaptive statistical approach for testing genetic associations of multiple traits from single/multiple studies using univariate GWAS summary statistics.
User: raydebashree
genome-analysis,Scripts and procedures for detecting positively selected genes and codons in primates
User: robinvanderlee
Home Page: https://doi.org/10.1093/nar/gkx704
genome-analysis,Library-free horizontal transfer detection, with a focus on transposable element invasions
User: rpianezza
genome-analysis,A python project for analysis of codon usage for gene or genome analysis
User: souradiptoc
Home Page: https://github.com/SouradiptoC/CodonU
genome-analysis,Earl Grey: A fully automated TE curation and annotation pipeline
User: tobybaril
genome-analysis,NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
Organization: wglab
genome-analysis,Fast Bayesian Hidden Markov Model with Wavelet Compression
User: wiedenhoeft
Home Page: http://wiedenhoeft.github.io/HaMMLET/
genome-analysis,For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics
Organization: wurmlab
Home Page: https://wurmlab.com/genomicscourse/
genome-analysis,A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline
User: zhuxitong
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