Jtrachsel

Jtrachsel's Stars

• tidyomics/plyranges

  A grammar of genomic data transformation

  Language:R13818

• tidyomics/tidyomics

  Easily install and load packages from the tidyomcis ecosystem

  Language:R60

• ksahlin/strobealign

  Aligns short reads using dynamic seed size with strobemers

  Language:C++14117

• scikit-bio/scikit-bio

  scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

  Language:Python881268

• vegandevs/vegan

  R package for community ecologists: popular ordination methods, ecological null models & diversity analysis

  Language:R44897

• arumugamlab/msamtools

  Metagenomics-related extended functionalities to samtools

  Language:C182

• cultivarium/GenomeSPOT

  Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome

  Language:Jupyter Notebook342

• shenwei356/taxonkit

  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

  Language:Go36929

• goodekat/ggResidpanel

  An R package for creating a panel of diagnostic plots for residuals from a model.

  Language:R363

• tseemann/snippy

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

  Language:Perl468114

• vgl-hub/gfastats

  A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation.

  Language:C++918

• k5cents/gluedown

  Wrap R vectors in markdown syntax

  Language:R1151

• Jtrachsel/pdtools

  Functions for working with NCBI's Pathogen Detection data

  Language:R2

• donkeyshot/phybreak

  Outbreak reconstruction with sequence data

  Language:R89

• USDA-ARS-GBRU/GuideMaker

  GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

  Language:Python63

• carlmurie/NOMAD

  MSMS normalization

  Language:R41

• seq-code/seqcode

  The International Code of Nomenclature of Prokaryotes Described from Sequence Data

  5

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R58765

• sevvandi/lookout

  Language:R30

• alvinxhan/PhyCLIP

  Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)

  Language:Python155

• alvinxhan/Phydelity

  Inference of putative transmission phylogenetic clusters

  Language:Jupyter Notebook111

• spacegraphcats/spacegraphcats

  Indexing & querying large assembly graphs -- in space, no one can hear you miao!

  Language:Standard ML11615

• dwinter/pafr

  Read, manipulate and visualize 'Pairwise mApping Format' data in R

  Language:R659

• merenlab/anvio

  An analysis and visualization platform for 'omics data

  Language:Python431145

• michaelkyu/PlasX

  PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

  Language:Python281

• lasy/alto

  'alto' is an R package that aligns topics from different LDA models, computes metrics for quantifying the goodness of alignment, and provides visualization functions to explore the alignment and robustness of topics across environments or LDA hyper-parameters.

  Language:R143

• kylebittinger/usedist

  Functions for distance matrix objects in R.

  Language:R146

• jtamames/SqueezeMeta

  A complete pipeline for metagenomic analysis

  Language:C37179

• FrederickHuangLin/ANCOMBC

  Differential abundance (DA) and correlation analyses for microbial absolute abundance data

  Language:R10428

• ablab/spades

  SPAdes Genome Assembler

  Language:C++739134