119 tool(s) found

Tool Description Topics Available version(s)
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
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 2
Change Case of selected columns 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 Biom datasets 1
Convert CSV to tabular 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 2
Convert FASTA to Bowtie color space Index 2
Convert FASTA to fai file 1
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
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to BAM without sorting 1
Convert tabular to CSV 1
Convert tabular to dbnsfp 2
Convert tar to directory 2
Convert uncompressed BCF to BCF 1
Count occurrences of each record 2
Create single interval as a new dataset 1
Data Fetch Query and retrieval 1
DAVID functional annotation for a list of genes 1
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 3
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
Filter data on any column using simple expressions Formatting 2
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
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 2
Group data by a column and perform aggregate operation on other columns. 4
InChI to MOL 3
Inchi to sink Convert InChI input to CSV sink 1
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 3
OpenBabel converter for molecular formats 1
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
SbmlToSbol Convert sbml to sbol format 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 3
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
Sort data in ascending or descending order 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
Summary Statistics for any numerical column 3
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