Galaxy | Repositories Owned by bebatut

Repositories Owned by bebatut

Name↓	Synopsis	Type	Metadata Revisions	Category
cdhit	Cd-Hit is a very widely used program for clustering and comparing protein or nucleotide sequences	Unrestricted	1 (2018-05-04)	Fasta Manipulation Sequence Analysis
combine_metaphlan2_humann2	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	Unrestricted		Metagenomics
compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	Unrestricted		Metagenomics
compute_wilcoxon_test	Compute Wilcoxon test with R	Unrestricted	0 (2016-04-21)	Statistics
convert_extract_sequence_file	Convert/ Extract information from a sequence file, with possible constraints	Unrestricted	1 (2016-04-28)	Fasta Manipulation Fastq Manipulation
export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	Unrestricted	1 (2016-06-21)	Metagenomics
extract_min_max_lines	Extract lines corresponding with minimum and maximum values of a column	Unrestricted	0 (2016-04-15)	Text Manipulation
fasta_add_barcode	Add barcodes at begining of FASTA sequences	Unrestricted	0 (2016-04-15)	Fasta Manipulation
format_cd_hit_output	Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file	Unrestricted		Fasta Manipulation
format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	Unrestricted		Metagenomics
graphlan	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	Unrestricted	0 (2016-05-26)	Metagenomics Graphics Phylogenetics
group_humann2_uniref_abundances_to_go	Group abundances of UniRef50 gene families obtained with HUMAnN2 to Gene Ontology (GO) slim terms with relative abundances	Unrestricted		Metagenomics
humann2	HUMAnN2 is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.	Unrestricted		Metagenomics
metaphlan2	MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution	Unrestricted	1 (2016-06-16)	Metagenomics
normalize_dataset	Normalize a dataset by row or column sum	Unrestricted	0 (2016-04-15)	Text Manipulation
package_goatools_0_6_4	Contains a tool dependency definition that downloads and compiles version 0.6.4 of python goatools package as well as scripts	Tool dependency definition	0 (2016-05-27)	Tool Dependency Packages
package_humann2_0_6_1	HUMAnN2 is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.	Tool dependency definition	0 (2016-05-26)	Tool Dependency Packages
package_metaphlan2_2_2_0	MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution	Tool dependency definition	0 (2016-05-26)	Tool Dependency Packages
package_metaphlan2_2_5_0	MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution	Tool dependency definition	0 (2016-06-01)	Tool Dependency Packages
package_r_3_2_1_getopt_1_20_0	Contains a tool dependency definition that downloads and installs version 1.20.0 of the getopt R library	Tool dependency definition	0 (2016-04-18)	Tool Dependency Packages
plot_barplot	Plot a barplot graphic using R	Unrestricted	1 (2016-05-18)	Visualization
plot_generic_x_y_plot	Plot a generic X-Y plot graphic using R	Unrestricted	0 (2016-04-18)	Visualization
plot_grouped_barplot	Plot a grouped barplot graphic using R	Unrestricted	0 (2016-04-18)	Visualization

Name↓

Synopsis

Type

Metadata
Revisions

Category

cdhit

Cd-Hit is a very widely used program for clustering and comparing protein or nucleotide sequences

Unrestricted

1 (2018-05-04)

combine_metaphlan2_humann2

Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances

Unrestricted

Metagenomics

compare_humann2_output

Compare outputs of HUMAnN2 for several samples and extract similar and specific information

Unrestricted

Metagenomics

compute_wilcoxon_test

Compute Wilcoxon test with R

Unrestricted

0 (2016-04-21)

Statistics

convert_extract_sequence_file

Convert/ Extract information from a sequence file, with possible constraints

Unrestricted

1 (2016-04-28)

export2graphlan

export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn

Unrestricted

1 (2016-06-21)

Metagenomics

extract_min_max_lines

Extract lines corresponding with minimum and maximum values of a column

Unrestricted

0 (2016-04-15)

Text Manipulation

fasta_add_barcode

Add barcodes at begining of FASTA sequences

Unrestricted

0 (2016-04-15)

Fasta Manipulation

format_cd_hit_output

Format CD-hit output to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file

Unrestricted

Fasta Manipulation

format_metaphlan2_output

Format MetaPhlAn2 output to extract abundance at different taxonomic levels

Unrestricted

Metagenomics

graphlan

GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees

Unrestricted

0 (2016-05-26)

group_humann2_uniref_abundances_to_go

Group abundances of UniRef50 gene families obtained with HUMAnN2 to Gene Ontology (GO) slim terms with relative abundances

Unrestricted

Metagenomics

humann2

HUMAnN2 is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Unrestricted

Metagenomics

metaphlan2

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution

Unrestricted

1 (2016-06-16)

Metagenomics

normalize_dataset

Normalize a dataset by row or column sum

Unrestricted

0 (2016-04-15)

Text Manipulation

package_goatools_0_6_4

Contains a tool dependency definition that downloads and compiles version 0.6.4 of python goatools package as well as scripts

Tool dependency definition

0 (2016-05-27)

Tool Dependency Packages

package_humann2_0_6_1

HUMAnN2 is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.

Tool dependency definition

0 (2016-05-26)