jjsekela

jjsekela's Stars

• Gibbons-Lab/isb_course_2022

  Materials and presentation for the 2022 ISB Microbiome course.

  Language:Jupyter Notebook2713

• ComparativeGenomicsToolkit/cactus

  Official home of genome aligner based upon notion of Cactus graphs

  Language:C521111

• gsneha26/SegAlign

  A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043

  Language:C++6616

• picrust/picrust2

  Code, unit tests, and tutorials for running PICRUSt2

  Language:Python329104

• BenLangmead/bowtie2

  A fast and sensitive gapped read aligner

  Language:C++681159

• soedinglab/MMseqs2

  MMseqs2: ultra fast and sensitive search and clustering suite

  Language:C1.4k195

• sarisabban/RMSD

  Calculate the RMSD between two protein structures

  Language:Python10

• charnley/rmsd

  Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

  Language:Python500114

• genometools/genometools

  GenomeTools genome analysis system.

  Language:C29664

• talgalili/heatmaply

  Interactive Heat Maps for R Using plotly

  Language:R37873

• XiaoLuo-boy/ggheatmap

  ggplot2 version of heatmap

  Language:R8412

• tttianhao/CLEAN

  CLEAN: a contrastive learning model for high-quality functional prediction of proteins

  Language:Python22545

• PombertLab/3DFI

  The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

  Language:Perl187

• YoshitakaMo/localcolabfold

  ColabFold on your local PC

  Language:Python600134

• mamba-org/micromamba-docker

  Rapid builds of small Conda-based containers using micromamba.

  Language:Shell26745

• conda-forge/staged-recipes

  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Language:Python7105k

• ossu/bioinformatics

  :microscope: Path to a free self-taught education in Bioinformatics!

  5.5k922

• rcedgar/muscle

  Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

  Language:C++21223

• jjsekela/tutorial-template_jjs

  Template for the Read the Docs tutorial

  1

• pachterlab/gget

  🧬 gget enables efficient querying of genomic reference databases

  Language:Python94674

• fteufel/signalp-6.0

  Multi-class signal peptide prediction and structure decoding model.

  Language:Python8315

• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  Language:Python570106

• compomics/meta-proteome-analyzer

  MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.

  Language:TSQL2710

• sortmerna/sortmerna

  SortMeRNA: next-generation sequence filtering and alignment tool

  Language:C++24568

• trinityrnaseq/trinityrnaseq

  Trinity RNA-Seq de novo transcriptome assembly

  Language:Perl835320

• conda-forge/miniforge

  A conda-forge distribution.

  Language:Shell6.5k331

• loneknightpy/idba

  Language:C++12453

• markfairbanks/tidypolars

  Tidy interface to polars

  Language:Python34311

• Ruunyox/slurmvision

  TUI for browsing, canceling, and inspecting SLURM jobs

  Language:Python101

• ankuanand/Algorithms

  Books on Algorothms

  Language:Ruby5124