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 2
BED-to-GFF converter Conversion 1
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 2
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 2
Convert FASTA to Tabular 1
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 SAM to BAM 1
Convert tabular to dbnsfp 2
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 9
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 10
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 8
Cuffmerge merge together several Cufflinks assemblies 8
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. 5
GTF-to-BEDGraph converter Conversion 1
GTF_to_GFF3 converter 1
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 4
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 2
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 10
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 RNA-Seq data 12
Upload File from your computer 2
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 2
Wiggle-to-Interval converter 2