175 tool(s) found

Tool Description Topics Available version(s)
(0) Examples and Instructions Instructions on how to use the KIRMES modular prediction and classification tools, including examples with predefined datasets. 1
(1) INCLUSive MotifSampler Find over-represented motifs in a FASTA file 1
(1) KIRMES K-Mer Counting Find over-represented motifs using a k-mer counting strategy 1
(1) PRIORITY Gibbs Sampler Find over-represented motifs using Raluca Gordan's PRIORITY program 1
(2) Prepare Prediction Dataset Find a set of motifs in a FASTA file 1
(3) KIRMES Training and Prediction Trains KIRMES using a set of positive and negative regulatory regions 1
Add column to an existing dataset 3
Analyze Alignment Error 1
Analyze Error Model 1
Anno2ContentLabel Generates labeled content segments from an annotation 1
Anno2SignalLabel Generates labeled positions from an annotation gene structure (AGS) 1
Artificial spliced reads from GFF and Fastq 1
ARTS Accurate transcription start site prediction 1
ASP Accurate splice site prediction 1
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED_to_GFF3 converter 3
Bowtie2 - map reads against reference genome 21
Change Case of selected columns 1
CloudGen (ARFF) Generation of a toy data set 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Compare to Optimal Alignment 1
Compare two Datasets to find common or distinct rows 1
ComposeMGenePredictor Creates a complete mGene predictor object from the various parts 1
Concatenate datasets tail-to-head 1
ContentEval Computes performance measures based on content (segment) labels and predictions 1
ContentPredict Applies a trained content predictor to the whole genome 1
ContentTrain Trains a content predictor using a set of labeled segments 1
Convert delimiters to TAB 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
Create error model 1
Create single interval as a new dataset 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 14
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cut columns from a table 2
DESeq Determines differentially expressed transcripts from read alignments 3
DESeq2 Differential gene expression analysis based on the negative binomial distribution 2
Detect isoforms using SplAdder Detection of new RNA-seq confirmed isoforms with SplAdder 1
DEXSeq Inference of differential exon usage in RNA-Seq 2
edgeR Empirical analysis of digital gene expression data in R 1
Evaluate mTIM transcript predictions Evaluation of mTIM transcript predictions 1
Evaluate Predictions Use predictions and labeled examples to measure prediction performance 1
Examine_GFF file Parent-Child relations 1
Examples and Instructions Instructions on how to use the mGene tools with predefined datasets 1
Examples and Instructions Instructions on how to use the mTIM tools and examples with predefined datasets 1
Examples and Instructions (v0.2) Instructions on how to use the mGene monolithic tools and examples with predefined datasets 1
Extract features from GFF data 1
FeatureScan gives an overview about GFF feature content 1
Filter data on any column using simple expressions Formatting 1
Filter GTF data by attribute values_list 1
GBK-to-GFF converter 2
GeneEval Computes performance measures based on gene labels and predictions 1
GenePredict Genome-wide gene prediction using the trained mGene system 1
GeneSetter plots family of diff. or not or expressed genes 1
GeneTrain Trains mGene using set of known genes and signal predictions 1
GenomeTool Creates a genome information object (GIO) from FASTA sequences 1
Get Microbial Data 1
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 2
GTF-to-BEDGraph converter Conversion 1
GTF_to_GFF3 converter 2
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Infer ORFs using SplAdder Inference of Open Reading Frames using InferORF 1
Join two Datasets side by side on a specified field 2
LAV to BED Converts a LAV formatted file to BED format 1
Line/Word/Character count of a dataset 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
Map with BFAST 1
Map with BWA for Illumina 4
Map with GenomeMapper 1
Map with Mosaik 1
Map with PALMapper 1
Map with PALMapper 1
Map with PerM for SOLiD and Illumina 1
Merge Columns together 2
mGene_GFFParser Generates an annotation gene structure object (AGS) 1
mGeneEval (v0.2) Computes performance measures based on gene labels and predictions 1
mGenePredict (v0.2) Predicts genes using a trained mGene system 1
mGeneTrain (v0.2) Trains mGene using set of known genes 1
MMR Multiple Mapper Resolution 1
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
MotifGen (ARFF) Generation of a sequence toy data set for motif discovery in ARFF format. 1
MotifGen (FASTA) Generation of a sequence toy data set for motif discovery in FASTA format. 1
mTIM-Train data preparation and training 1
NuPoP Predict nucleosome positioning for DNA sequences of any length 1
Paste two files side by side 1
Positional Oligomer Matrices Visualize SVMs with WD kernel 1
Predict using mTIM Genome-wide prediction with mTIM 1
Random subset of FASTQ 1
rDiff Determines differentially expressed transcripts from read alignments 1
Re-align with SRMA 1
Remove beginning of a file 1
RiboDiff Detect protein translational efficiency difference 1
rQuant Determines transcript abundance from read alignments 1
SAFT Simple Alignment Filtering Tool 1
Scripture ab initio transcriptome reconstruction from RNA-Seq reads 1
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 first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
SFF converter 1
SignalEval Computes performance measures based on signal labels and predictions 1
SignalPredict Applies a trained signal predictor to the whole genome 1
SignalTrain Trains a signal predictor using a set of labeled positions 1
SInBaD Exploring functional variant discovery in non-coding regions 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
SplicePredict (v0.2) Predicts splice sites on the whole genome 1
STAR RNA-seq read mapper 1
SVM Model Selection Find the best combination of SVM hyper-parameters 1
topGO Enrichment analysis for Gene Ontology 1
TopHat Gapped-read mapper for RNA-seq data 12
Tophat for Illumina Find splice junctions using RNA-seq data 3
Train and Test SVMs Train SVMs and predict for given hyper-parameters 1
Train QPALMA 1
Trim leading or trailing characters 1
Trinity De novo assembly of transcriptome from RNA-Seq data 10
Upload File from your computer 2
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1