fplazaonate

Microbiome data scientist

INRAE MetaGenoPolisFrance

Pinned Repositories

csfasta-fasta-conv
Program that converts files from csfasta format to fasta and the other way around.
Language:C++1 2 00
fasta-utils
Set of tools to manipulate and compute statistics on FASTA files
Language:Python1 2 00
fastq-qual-stats
Tool that computes statistics on sequencing data.
Language:C++1 2 00
fastq-sample
Language:C++4 2 01
mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
Language:C++12 4 55
sequence-translator
Translate DNA or RNA sequences to protein sequences.
Language:C++2 2 01
xsq-convert
xsq-convert converts Solid XSQ files to csfasta/qual files
Language:C++4 2 21
CroCoDeEL
CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data
Language:Python10 2 20
ESKRIM
ESKRIM is a reference-free tool that compares microbial richness in shotgun metagenomic samples by counting k-mers
Language:Python4 1 00
meteor
Meteor is a plateform for quantitative metagenomics profiling of complex ecosystems. Meteor relies on genes catalogue to perform species-level taxonomic profiling (Bacteria, Archaea and Eukaryotes), functional analysis and strain-level population structure inference.
Language:Python14 4 430

fplazaonate's Repositories

fplazaonate/mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
Language:C++12 4 55
fplazaonate/fastq-sample
Language:C++4 2 01
fplazaonate/xsq-convert
xsq-convert converts Solid XSQ files to csfasta/qual files
Language:C++4 2 21
fplazaonate/sequence-translator
Translate DNA or RNA sequences to protein sequences.
Language:C++2 2 01
fplazaonate/csfasta-fasta-conv
Program that converts files from csfasta format to fasta and the other way around.
Language:C++1 2 00
fplazaonate/fasta-utils
Set of tools to manipulate and compute statistics on FASTA files
Language:Python1 2 00
fplazaonate/fastq-qual-stats
Tool that computes statistics on sequencing data.
Language:C++1 2 00
fplazaonate/mgs-scripts
Language:Python1 2 0
fplazaonate/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
fplazaonate/compute-cormat
Compute large correlation matrix with BLAS routines
Language:C++2 0
fplazaonate/count-genes-connections
Language:C++2 0
fplazaonate/count_matrix_to_sqlite_db
Language:Python2 0
fplazaonate/CountMatrixDownsizer
Rarefies OTUs or genes raw abundance profiles to even sequencing depth across samples.
Language:C++2 0
fplazaonate/CountMatrixTransformer
Compute relative gene abundance from raw read counts
Language:C++2 0
fplazaonate/cppstats
Language:C++2 0
fplazaonate/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Language:C++0 0
fplazaonate/fetch-cscg
Language:Python2 0
fplazaonate/merge-cdhit-clusters
Language:C++2 0
fplazaonate/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Language:Python1 0
fplazaonate/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
Language:Python0 0
fplazaonate/precompute-cormat
Compute large correlation matrix with BLAS routines
Language:C++2 0
fplazaonate/qn_stat
C implementation of Rousseeuw and Croux' Qn robust measure of scale
Language:C2 02
fplazaonate/Rcpp
Seamless R and C++ Integration
Language:C++2 0
fplazaonate/SamplesDissimilarity
Language:C++
fplazaonate/sort-fastq-by-length
Language:C++2 0
fplazaonate/sort-fastq-by-quality
Language:C++
fplazaonate/split_fasta
Split fasta file in multiple files depending on the size or on your will.
Language:Python2 0
fplazaonate/trim_fastq
Language:Python2 0
fplazaonate/Well2WellContaminationPublication
Language:Jupyter Notebook0 0
fplazaonate/xsq-info
xsq-info reads and prints information (metadata, number of reads) from a XSQ file
Language:C++2 0