Pinned Repositories
ab_genomed_qc
Assess Acinetobacter baumannii genomes quality on the nucleotide level
add_locustag_gbk_embl
Adds locus tag to GenBank and EMBL format files.
evo-ngs-refprep
Preparation of reference genome for variant calling pipeline
get_taxonomy_by_NCBI_TaxID
Get linage string by NCBI TaxID
ijump
Software to search rearrangements in population sequencing data
metaphlan2_to_qiime
Convert Metaphlan2 format to QIIME format
morbidostat_construction
Building Osterman Lab implementation of morbidostat
morbidostat_v2_construction
patric_gto_tools
Scripts to convert PATRIC gto format to other formats
Triclosan_EE_paper
Experimental evolution of E. coli with exposure to triclosan
sleyn's Repositories
sleyn/morbidostat_construction
Building Osterman Lab implementation of morbidostat
sleyn/ijump
Software to search rearrangements in population sequencing data
sleyn/evo-ngs-refprep
Preparation of reference genome for variant calling pipeline
sleyn/get_taxonomy_by_NCBI_TaxID
Get linage string by NCBI TaxID
sleyn/metaphlan2_to_qiime
Convert Metaphlan2 format to QIIME format
sleyn/morbidostat_v2_construction
sleyn/patric_gto_tools
Scripts to convert PATRIC gto format to other formats
sleyn/Triclosan_EE_paper
Experimental evolution of E. coli with exposure to triclosan
sleyn/ab_genomed_qc
Assess Acinetobacter baumannii genomes quality on the nucleotide level
sleyn/add_locustag_gbk_embl
Adds locus tag to GenBank and EMBL format files.
sleyn/aln_stats_prot
Script producing protein alignment variants statistics
sleyn/d3
Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:
sleyn/demux_i7
Demultiplex paired-end reads based only the i7 index
sleyn/docker_patric_cli_1.039
Dockerized version of PATRIC CLI v.1.039
sleyn/extract_aln_columns
Extracts columns from alignment according to positions in the reference sequence.
sleyn/github-slideshow
A robot powered training repository :robot:
sleyn/ISfinder-sequences
Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)
sleyn/MoRbido
R package for processing morbidostat v.1 log files
sleyn/panmap
nucmer wrapper for mapping multiple close related genomes on a reference
sleyn/paper_cipro_EC_AB_PA_2021
Supplementary code for "Morbidostat-Directed Experimental Evolution of Ciprofloxacin Resistance in Gram-negative Bacterial Pathogens" paper.
sleyn/subpop_decompose_gd
Decomposition of population deep-sequencing data into subpopulations using gradient descend algorithm.
sleyn/subpop_decompose_mip
Decompose observed variants to subpopulations using mixed integer programming with pulp package,
sleyn/U50
U50 : measuring assembly output based on non-overlapping, target-specific contigs
sleyn/wordly_helper
Shiny app aims to help choose words for WORDLY game