131 tool(s) found

Tool Description Topics Available version(s)
A) Format Data for LEfSe 2
Add column to an existing dataset 3
Add rings to the tree 1
Aggregate datapoints such as phastCons, GERP, binCons, and others for a set of genomic intervals 1
Annotate tree 2
B) LDA Effect Size (LEfSe) 2
BEAM significant single- and multi-locus SNP associations in case-control studies 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
Boxplot of quality statistics 1
C) Plot LEfSe Results 2
Categorize by function 1
Change Case of selected columns 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Compare two Datasets to find common or distinct rows 1
Compute quality statistics for SOLiD data 1
Condense consecutive characters 2
Convert delimiters to TAB 1
Convert SOLiD output to fastq 1
Convert BCF to BCF_BGZIP 1
Convert BCF_BGZIP to BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Count occurrences of each record 1
Create single interval as a new dataset 1
D) Plot Cladogram 2
DAVID functional annotation for a list of genes 1
Draw quality score boxplot for SOLiD data 1
E) Plot One Feature 2
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 1
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
F) Plot Differential Features 2
Filter data on any column using simple expressions Formatting 1
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 1
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 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
GPASS significant single-SNP associations in case-control studies 1
Group data by a column and perform aggregate operation on other columns. 2
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 2
LD linkage disequilibrium and tag SNPs 1
Line/Word/Character count of a dataset 1
LPS LASSO-Patternsearch algorithm 1
MaAsLin 1
MAF Coverage Stats Alignment coverage information 1
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 2
MetaPhlAn metagenomic profiler 2
MetaPhlAn2 metagenomic profiler V2 2
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
Normalize By Copy Number 1
PASS significant transcription factor binding sites from ChIP data 1
Paste two files side by side 1
Plot tree 2
Predict Metagenome 1
Remove beginning of a file 1
Reverse Complement a MAF file 1
Run micropita 3
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select random lines from a file 2
SFF converter 1
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Sort data in ascending or descending order 2
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
Summary Statistics for any numerical column 3
Trim leading or trailing characters 1
Upload File from your computer 2
VCF to MAF Custom Track for display at UCSC 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1