Pinned Repositories
abundance_filters
Mutlidimension abundance filter: per sample, across dataset, on selected or fractions of samples or replicates
amplicon_pipeline
An analysis pipeline for paired end amplicon sequencing
Dataset_properties_distances
A jupyter notebook in development to get distances between datasets for analytic methods/parameters prediction
metagenomix
A pipeline of pipelines to conduct metagenomic analyses on Slurm/Torque
microbiome_analyzer
Command line tool that writes commands to run one by one to perform analyses (mainly using qiime2) on a HPC running Slurm, Torque or none of these.
mistag_filter
Metabarcoding sequence abundance filter for projects involving combinations of short tagged primers for the labeling of amplicons and samples multiplexing
q2-metadata
Xclusion_criteria
Generate interactive, user-defined visualisations to help defining inclusion/exclusion criteria on a metadata table
Xpbs
Convert of .sh script into Torque's .pbs or Slurm's script for use on a computer cluster with intel or gpu nodes
Xrbfetch
Fetch microbiome tables using RedBiom based on a metadata file and filter (i) blooms, (ii) read-sum based and (iii) duplicate hosts and preps (only for Qiita/AGP)
FranckLejzerowicz's Repositories
FranckLejzerowicz/metagenomix
A pipeline of pipelines to conduct metagenomic analyses on Slurm/Torque
FranckLejzerowicz/mistag_filter
Metabarcoding sequence abundance filter for projects involving combinations of short tagged primers for the labeling of amplicons and samples multiplexing
FranckLejzerowicz/microbiome_analyzer
Command line tool that writes commands to run one by one to perform analyses (mainly using qiime2) on a HPC running Slurm, Torque or none of these.
FranckLejzerowicz/Xpbs
Convert of .sh script into Torque's .pbs or Slurm's script for use on a computer cluster with intel or gpu nodes
FranckLejzerowicz/q2-metadata
FranckLejzerowicz/Xclusion_criteria
Generate interactive, user-defined visualisations to help defining inclusion/exclusion criteria on a metadata table
FranckLejzerowicz/Xrbfetch
Fetch microbiome tables using RedBiom based on a metadata file and filter (i) blooms, (ii) read-sum based and (iii) duplicate hosts and preps (only for Qiita/AGP)
FranckLejzerowicz/evaluate_dada2
Explore various trim lengths to fit one or more mock sample(s)
FranckLejzerowicz/FranckLejzerowicz.github.io
Personal website for Franck Lejzerowicz
FranckLejzerowicz/microsetta-interface
The Microsetta participant facing user interface
FranckLejzerowicz/MIDAS2
Metagenomic Intra-Species Diversity Analysis 2
FranckLejzerowicz/polyGs_stats
count reads and polyGs and get the motifs before the Gs
FranckLejzerowicz/prep_songbird
Generate scripts for QIIME2's songbird to run multinomial regression models defined in a config file, for many datasets, subsets, filtering version, and run parameters, including train-test columns and baselines
FranckLejzerowicz/q2-deblur
FranckLejzerowicz/q2-taxa
FranckLejzerowicz/scikit-bio
scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.
FranckLejzerowicz/songbird
Vanilla regression methods for microbiome differential abundance analysis
FranckLejzerowicz/woltka
Web of Life Toolkit App
FranckLejzerowicz/XDOC
A python wrapper of the R wrapper from https://github.com/Russel88/DOC to run the DOC analysis
FranckLejzerowicz/Xhpc
Convert of .sh script into Torque's .pbs or Slurm's script for use on a computer cluster with intel or gpu nodes
FranckLejzerowicz/XMCA
Perform MCA analysis from metadata and obtain and interactive html plot, including variables selection and samples descriptions
FranckLejzerowicz/Xmmvec
Explore mmvec ranks results
FranckLejzerowicz/Xphate
Explore PHATE results
FranckLejzerowicz/Xplor_distros
Explore the distributions of the continuous data in your metadata file that you may want to analyse jointly.
FranckLejzerowicz/Xports
Simple export tool for all the files that have a given extension (retrieve, copy, archive, scp command)
FranckLejzerowicz/Xpress_parse
Help a user or a group of users to semi-automatically parse and select (and label) papers searched on Web Of Science based on their abstracts.
FranckLejzerowicz/Xsinfo
Summarize nodes and cores available for compute on a SLURM scheduler
FranckLejzerowicz/Xsourcetracking
Run FEAST, sourcetracker2 or ML classification for a features table, metadata and metadata column's sink (and sources) to help identifying most likely features origin and curate sample labeling
FranckLejzerowicz/Xtensorboard
to create a tunnel job for inspect tensorboard
FranckLejzerowicz/Xvert_docstring_plain2np
Convert docstring fro plain 2 NumPy format