| Add column |
to an existing dataset |
Editing
|
2 |
| Aggregate datapoints |
Appends the average, min, max of datapoints per interval |
|
2 |
| BasicDesign |
Build DNA-BOT input files from rpSBML |
|
1 |
| bcf_uncompressed-to-bcf |
converter |
|
1 |
| BED-to-bigBed |
converter |
Conversion
|
2 |
| BED-to-GFF |
converter |
Conversion
|
1 |
| biom2-to-biom1 |
converter |
|
1 |
| Change Case |
of selected columns |
|
2 |
| cml-to-mol2 |
converter |
|
1 |
| cml-to-smi |
converter |
|
2 |
| Compare two Datasets |
to find common or distinct rows |
Filtering
|
1 |
| Complete Reactions |
From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions |
|
1 |
| Condense |
consecutive characters |
|
2 |
| Convert |
delimiters to TAB |
|
1 |
| Convert BED to Feature Location Index |
|
|
1 |
| Convert BED to GFF |
|
|
2 |
| Convert FASTA to 2bit |
|
|
2 |
| Convert FASTA to Bowtie base space Index |
|
|
2 |
| Convert FASTA to Bowtie color space Index |
|
|
2 |
| Convert FASTA to len file |
|
|
2 |
| Convert FASTA to Tabular |
|
|
1 |
| Convert genome coordinates |
between assemblies and genomes |
|
2 |
| Convert Genomic Intervals To BED |
|
|
1 |
| Convert Genomic Intervals To Coverage |
|
|
2 |
| Convert Genomic Intervals To Strict BED |
|
|
2 |
| Convert Genomic Intervals To Strict BED12 |
|
|
1 |
| Convert Genomic Intervals To Strict BED6 |
|
|
2 |
| Convert GFF to BED |
|
|
2 |
| Convert GFF to Feature Location Index |
|
|
1 |
| Convert Len file to Linecount |
|
|
2 |
| Convert lped to fped |
|
|
2 |
| Convert lped to plink pbed |
|
|
2 |
| Convert MAF to Fasta |
|
|
2 |
| Convert MAF to Genomic Intervals |
|
|
2 |
| Convert Picard Interval List to BED6 |
converter |
|
2 |
| Convert plink pbed to ld reduced format |
|
|
2 |
| Convert plink pbed to linkage lped |
|
|
2 |
| Count |
occurrences of each record |
|
2 |
| Create single interval |
as a new dataset |
|
1 |
| csv-to-tabular |
converter |
|
1 |
| Data Fetch |
|
Query and retrieval
|
1 |
| DAVID |
functional annotation for a list of genes |
|
1 |
| dbnsfp.tabular-to-snpsiftdbnsfp |
converter |
|
3 |
| Design of Experiment |
An optimal design of experiments (DoE) base package for synthetic biology |
|
1 |
| DNA Weaver |
Given a SBOL input, calculate assembly parts for Gibson or Golden Gate |
|
1 |
| DNA-Bot |
DNA assembly using BASIC on OpenTrons |
|
1 |
| Export datasets |
to remote files source |
|
1 |
| Extract features |
from GFF data |
|
1 |
| Extract MAF blocks |
given a set of genomic intervals |
|
4 |
| Extract MAF by block number |
given a set of block numbers and a MAF file |
|
1 |
| Extract Pairwise MAF blocks |
given a set of genomic intervals |
|
1 |
| fasta-to-fai |
converter |
|
1 |
| Filter |
data on any column using simple expressions |
Formatting
|
2 |
| Filter GFF data by attribute |
using simple expressions |
|
2 |
| Filter GFF data by feature count |
using simple expressions |
|
1 |
| Filter GTF data by attribute values_list |
|
|
2 |
| Filter MAF |
by specified attributes |
|
1 |
| Filter MAF blocks |
by Species |
|
1 |
| Filter MAF blocks |
by Size |
|
1 |
| Flux balance analysis |
for the RetroPath2.0 heterologous pathways |
|
1 |
| g:Profiler |
tools for functional profiling of gene lists |
|
1 |
| Gene BED To Exon/Intron/Codon BED |
expander |
|
1 |
| GFF-to-BED |
converter |
Conversion
|
1 |
| Group |
data by a column and perform aggregate operation on other columns. |
|
4 |
| Inchi to sink |
Convert InChI input to CSV sink |
|
1 |
| inchi-to-mol |
converter |
|
2 |
| Join MAF blocks |
by Species |
|
1 |
| Join two Datasets |
side by side on a specified field |
|
4 |
| LCR Genie |
Ligase Chain Reaction |
|
1 |
| LD |
linkage disequilibrium and tag SNPs |
|
1 |
| Line/Word/Character count |
of a dataset |
|
1 |
| MAF Coverage Stats |
Alignment coverage information |
|
3 |
| MAF to BED |
Converts a MAF formatted file to the BED format |
|
1 |
| MAF to FASTA |
Converts a MAF formatted file to FASTA format |
|
1 |
| MAF to Interval |
Converts a MAF formatted file to the Interval format |
|
1 |
| MasterVar to pgSnp |
Convert from MasterVar to pgSnp format |
|
1 |
| Merge Columns |
together |
|
4 |
| mol2-to-mol |
converter |
|
2 |
| mothur.ref.taxonomy-to-mothur.seq.taxonomy |
converter |
|
2 |
| PartsGenie |
An integrated tool for optimizing and sharing synthetic biology parts |
|
1 |
| Paste |
two files side by side |
|
1 |
| Pathways HTML Report |
Generates HTML report to explore the main characteristics of pathwayspredicted with RetroPath suite |
|
1 |
| Pick SBML Model |
Pick an SBML model among a list |
|
1 |
| Rank Pathways |
Rank heterologous pathways according to their global score |
|
1 |
| Remove beginning |
of a file |
|
1 |
| RetroPath2.0 |
Build a reaction network from a set of source compounds to a set of sink compounds |
|
1 |
| Reverse Complement |
a MAF file |
|
1 |
| rp2biosensor |
Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output |
|
1 |
| RP2paths |
Enumerate and seperate the different pathways generated by RetroPath2.0 |
|
1 |
| RRules Parser |
Retrieve the reaction rules from RetroRules |
|
1 |
| sam-to-unsorted.bam |
converter |
|
1 |
| SbmlToSbol |
Convert sbml to sbol format |
|
1 |
| SBOL Converter |
Convert between SBOL3 and other genetic design formats |
|
1 |
| Score Pathway |
Computes a global score for a heterologous pathway. |
|
1 |
| Secure Hash / Message Digest |
on a dataset |
|
2 |
| Select |
lines that match an expression |
Filtering
|
3 |
| Select first |
lines from a dataset |
Filtering
|
4 |
| Select last |
lines from a dataset |
|
2 |
| Select random lines |
from a file |
|
2 |
| Selenzyme |
Performs enzyme selection from a reaction query |
|
1 |
| Send to cloud |
|
|
1 |
| SFF converter |
|
|
1 |
| Sink from SBML |
Generate the RetroPath2.0 sink file from an SBML input |
|
1 |
| smi-to-mol |
converter |
|
2 |
| smi-to-smi |
converter |
|
2 |
| Sort |
data in ascending or descending order |
Sorting
|
3 |
| Split MAF blocks |
by Species |
|
1 |
| Stitch Gene blocks |
given a set of coding exon intervals |
|
4 |
| Stitch MAF blocks |
given a set of genomic intervals |
|
1 |
| StrainDesign analyzing-model |
Produce a pareto plot for a biological model |
|
1 |
| StrainDesign reduce-model |
Delete gene in a biological model |
|
1 |
| StrainDesign simulate-deletion |
Search genes to delete in a biological model |
|
1 |
| Summary Statistics |
for any numerical column |
|
3 |
| tabular-to-csv |
converter |
|
1 |
| tar-to-directory |
converter |
|
2 |
| Thermo |
Calculate the formation energy of chemical species and the Gibbs free energy of their reactions and pathways in an SBML |
|
1 |
| Trim |
leading or trailing characters |
|
2 |
| Upload File |
from your computer |
Query and retrieval
|
3 |
| VCF to MAF Custom Track |
for display at UCSC |
|
2 |
| Visualize pathways |
Visualize pathways from the RetroPath Suite |
|
1 |
| Wig/BedGraph-to-bigWig |
converter |
|
2 |
| Wiggle to Interval |
|
|
2 |
| Wiggle-to-Interval |
converter |
|
2 |