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๐›๐š๐ซ๐›๐š๐œ is an R package designed for the ๐˜ฆ๐˜น๐˜ต๐˜ณ๐˜ข๐˜ค๐˜ต๐˜ช๐˜ฐ๐˜ฏ of barcode sequences. It efficiently ๐˜ค๐˜ญ๐˜ถ๐˜ด๐˜ต๐˜ฆ๐˜ณ๐˜ด these sequences and provides functionality for the calculation and visualization of ๐˜ต๐˜ช๐˜ฎ๐˜ฆ ๐˜ด๐˜ฆ๐˜ณ๐˜ช๐˜ฆ๐˜ด trajectories of the barcoded data.

License: Other

R 98.65% Dockerfile 1.35%
amplicon-sequencing clustering-algorithm metagenomics r-package

barbac's Introduction

barbac: an R package for barocde data analysis

barbac is a versatile R package tailor-made for researchers and bioinformaticians working with barcoded sequences. Whether you're delving into the vast realm of genomic data or investigating the temporal dynamics of molecular barcodes, barbac has got you covered.

Install the package using the following commands

Key Features:

  1. Barcode Extraction: Efficiently and accurately extract barcode sequences from your genomic datasets.

  2. Clustering of Barcodes: Group similar barcode sequences with the in-built clustering algorithm, providing meaningful insights into sequence families or operational taxonomic units (OTUs).

  3. Time Series Trajectories: Dive deep into the temporal dynamics of barcoded sequences. barbac not only calculates but also visually represents the trajectory of each barcode over time, making it easier to discern patterns, trends, and anomalies.

Applications:

  • Molecular Tracking: Monitor the abundance and variations of specific molecular barcodes over different time points.
  • Biodiversity Analysis: Understand the diversity and prevalence of barcode sequences in different samples.
  • Evolutionary Dynamics: Track and visualize the emergence, dominance, and decline of barcoded sequences across time.

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barbac's People

Contributors

loukesio avatar

Watchers

Kristian Ullrich avatar  avatar Carsten Fortmann-Grote avatar Thijs Janzen avatar  avatar

barbac's Issues

Add barcodes of high distance that might be missing

when you clustered Dave's data some barcodes were missing check out why!

  • One think is that the diagonal is not kept in pair_minsim
    and the other thing
  • What happens to the barcodes that have cluster but have the same counts? who wins

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