fplaza

Microbiome data scientist

INRAE MetaGenoPolisFrance

Pinned Repositories

CountMatrixDownsizer
Rarefies OTUs or genes raw abundance profiles to even sequencing depth across samples.
Language:C++00
CountMatrixTransformer
Compute relative gene abundance from raw read counts
Language:C++00
csfasta-fasta-conv
Program that converts files from csfasta format to fasta and the other way around.
Language:C++10
fasta-utils
Set of tools to manipulate and compute statistics on FASTA files
Language:Python10
fastq-qual-stats
Tool that computes statistics on sequencing data.
Language:C++10
fastq-sample
Language:C++4 2 01
mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
Language:C++11 4 55
mgs-scripts
Language:Python10
sequence-translator
Translate DNA or RNA sequences to protein sequences.
Language:C++21
xsq-convert
xsq-convert converts Solid XSQ files to csfasta/qual files
Language:C++41

fplaza's Repositories

fplaza/mgs-canopy-algorithm
Fork of the canopy clustering algorithm of Nielsen et al.
Language:C++11 4 55
fplaza/fastq-sample
Language:C++4 2 01
fplaza/sequence-translator
Translate DNA or RNA sequences to protein sequences.
Language:C++21
fplaza/fasta-utils
Set of tools to manipulate and compute statistics on FASTA files
Language:Python10
fplaza/mgs-scripts
Language:Python10
fplaza/CountMatrixDownsizer
Rarefies OTUs or genes raw abundance profiles to even sequencing depth across samples.
Language:C++00
fplaza/CountMatrixTransformer
Compute relative gene abundance from raw read counts
Language:C++00
fplaza/bowtie2
A fast and sensitive gapped read aligner
Language:C++
fplaza/CAMISIM
CAMISIM: Simulating metagenomes and microbial communities
Language:Python
fplaza/compute-cormat
Compute large correlation matrix with BLAS routines
Language:C++
fplaza/count_matrix_to_sqlite_db
Language:Python
fplaza/cppstats
Language:C++
fplaza/fetch-cscg
Language:Python
fplaza/FunctionnalAnnotation
Language:Python
fplaza/GTDBTk
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Language:Python
fplaza/KMC
Fast and frugal disk based k-mer counter
Language:C++
fplaza/merge-cdhit-clusters
Language:C++
fplaza/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
fplaza/mOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
Language:Python
fplaza/panphlan
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
fplaza/pb-metagenomics-tools
pb-metagenomics-tools
fplaza/precompute-cormat
Compute large correlation matrix with BLAS routines
Language:C++
fplaza/Rcpp
Seamless R and C++ Integration
Language:C++
fplaza/SamplesDissimilarity
Language:C++
fplaza/SemiBin
Language:Python
fplaza/sort-fastq-by-length
Language:C++
fplaza/sort-fastq-by-quality
Language:C++
fplaza/trim_fastq
Language:Python
fplaza/Well2WellContaminationPublication
Language:Jupyter Notebook
fplaza/xsq-info
xsq-info reads and prints information (metadata, number of reads) from a XSQ file
Language:C++