List of Applications
- mhelmke
- kkennedy
- dennis
Owned by mhelmke
Viewing the User Manual for an App
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- AAARF v 1.0.1
- add column to file
- add column to file2
- Add GO to Blastp-uniprot output
- Admixture
- AgBase GOanna 2.1
- ALLMAPS
- ALLMAPS merge
- ALLMAPS path
- AllpathsLG 44837
- AllpathsLG-small-genomes-44837
- Annotate transcripts
- AntEpiSeeker 2.0
- appendUnclustered
- Assembly Stats (assemblathon tool)
- Assess Assembly vs whole genome
- Ballgown-2.0
- Bam to Counts (general)
- BAM to Counts (named outputs)
- bayesembler-1.2
- Bayesian BiClustering
- BCFTOOLS-1.13 VCF-Utilities varFilter
- BCFtools 1.8 call
- BCFtools 1.8 index
- BCFtools 1.8 merge VCF
- BCFtools 1.8 query
- BCFtools 1.8 view
- BEAST-2.1.3
- BEAST 2.6.3
- BEAST2 on CyVerse UK
- BEAST on CyVerse UK
- BEDTools 2.26.0 bamToBed
- BEDTools 2.26.0 intersectBed
- BEDTools 2.26 fastaFromBed
- BEDTools 2.26 slopBed
- BEDTOOLS BAMtoFastq-2.26
- BEDTools coverageBed
- Bedtools Genome Coverage-BAM-2.26
- BEDTools genomeCoverageBed
- BEDTools maskFastaFromBed
- Best Hit for Blat Output
- bgzip
- Bismark
- Bismark Genome Preparation
- Bismark Methylation Extractor
- Blast2Seqs
- Blastdbcmd-batch-2.6.0
- Blastdbcmd-single-2.6.0
- Blastn-2.2.26
- Blastn-2.6.0+
- Blastp-2.2.29
- Blastp-2.6.0+
- BLASTp UniProt
- BLASTX (HPC)
- BLAT_psl_to_SAM
- Blat_with_BAM_output
- Blat (default)
- blat 36 (with options)
- Bowtie 1.2.2 build and map
- Bowtie-2.2.1--Build-and-Map
- Bowtie2-2.2.4 Bowtie2-Build indexer and aligner (HPC)
- Bowtie2Build-2.2.4 indexer
- Bowtie-Build
- btrim
- BuildICM-1.0.0-Dev
- Bulk Blast 2 Sequences
- BUSCO in the Discovery Environment
- BUSCO-v2.0 in the Discovery Environment
- BUSCO-v3.0 in the Discovery Environment
- BWA_mem_longreads-0.7.15
- BWA 0.7.12 indexer aligner and mem (HPC)
- BWA 0.7.4 Divergent species
- BWA-0.7.4 non-model species
- BWA Aligner for Paired-End Illumina Reads
- BWA Aligner for Single-End Illumina Reads
- BWA aln 0.7.4
- BWA index 0.7.4
- BWA mem 0.7.15
- bzip2 and bunzip2
- CACE
- Calling SNPs INDELs with SAMtools BCFtools
- Canberra Distance
- Canu 1.8
- CD-HIT-est 4.6.8
- CEGMA
- CharaParser Learn
- CharaParser Markup
- Check covariance matrix file (CheckCvm)
- Check standard GWAS files (CheckGwas)
- chloroExtractor 1.0.9
- Chromatra L
- Chromatra T
- Clean_fasta_header
- ClustalW2
- clusterProfiler
- clusterReport
- CNVnator-0.3.3
- combine GAFs
- Compress a directory with GNU tar-1.27.1
- Compress files with gzip 1.6-2
- Compress selected files with GNU tar
- Compute Contig Statistics
- Concatenate 2 Files-workflow edition.
- Concatenate Multiple Files
- construction genetic map
- Convert bwt to arf
- Convert SAM-to-sorted-BAM
- ConvertTraitID 0.0.1
- Copy with Scaffolding XML of DESeq2 (multifactorial pairwise comparisons)
- Create_BLAST_database-2.6.0__with_parse_seqids_option
- Create BLAST database
- Create BLAST database-2.6.0+
- create dir
- Cuffcompare-2.2.1
- Cuffdiff
- Cuffdiff2
- CuffDiff 2.2.1a
- Cuffdiff2-16-way-max
- Cuffdiff2 with JS option
- Cufflinks
- Cufflinks_from_SAM-2.2.1 in DE
- Cufflinks 2.2.1
- Cuffmerge2
- Cuffmerge 2.2.1
- curl-7.45.0
- cutadapt
- Cut Columns
- DataHog
- De-interlace paired fasta
- DeltaBLAST-2.2.29+
- de novo population genomics analysis
- DESeq
- DESeq2
- DESeq2 (multifactorial pairwise comparisons)
- DIAMOND 0.9.10
- DIAMOND-makedb-0.9.10
- DNANJ
- DNAPARS
- dos2unix
- Downsample reads
- draw Venn diagrams
- DREME 5.0.5
- DynamicTrim
- edgeR (multifactorial pairwise comparisons) in DE
- edgeR with Fisher's Exact Test
- EMBOSS cpgplot
- EMBOSS Cusp
- EMBOSS Seqret
- Emboss transeq
- Enhanced R Script
- evolinc
- Evolinc_merge-1.0
- Evolinc in the Discovery Environment
- Exonerate 2.2.0
- Extract First Lines From a File
- Extract Last Lines From a File
- FALCON (Small Genomes) 0.4.2
- FALCON-formatter
- FASTA Minimum Size Filter
- fastaRename
- FaST-LMM-2.07
- FastLMM Result Plotter
- FaST-LMM Results Plotter 2
- FaST-LMM Reults Plotter 2
- Fastp 0.20.1
- FASTQ_SHRINKER
- FastQC
- FastQC (demo)
- FastQC 0.10.1 (multi-file)
- FastQC-0.11.5 (multi-file)
- fastqCombinePariedEnd
- FastQC-plus 0.10.1 (multi-file)
- Fastq-Join
- Fastq-multx-1.4.0
- Fastq-Sample-0.8
- Fastq-screen-0.11.1
- Fastq-screen-0.4.4
- FastTree2
- FastTree Dispatcher 2.1.4
- FASTX Barcode Splitter
- FASTX Clipper 0.0.14
- Fastx Collapser
- FASTX fastq quality filter 0.0.14
- FASTX fastq to fasta 0.0.14
- FASTX quality filter and trim
- FASTX Quality Trimmer
- FASTX Toolkit
- FASTX Trimmer 0.0.14
- File_Select v1.0
- File_Split v1.0
- Filter_CuffDiff_Results
- Filter homozygous SNPs
- filter pileup
- Final filter
- Final filter2
- Find Lines Matching a Regular Expression
- Find SNPS - mpileup
- flattenClusters 1.0
- Fluorescent Imaging Pipeline (FLIP)
- Freebayes-0.9.20
- GapCloser 1.12
- GATK CombineGCVFs-3.2.2
- GATK GenotypeGVCFs-3.2.2
- GATK HaplotypeCaller
- GATK UnifiedGenotyper-3.2.2
- gbsAlign_BWA 0.5.9
- gbsFilter_TASSEL 3.0.133
- gbsMergeSNP_TASSEL 3.0.133
- gbsTags_TASSEL 3.0.133
- gbsTagsToSNP_TASSEL 3.0.133
- GBS Workflow
- GBS Workflow with user genome
- Generate detectability cartoons for syntenic features
- GeneSeqer_5.0
- GeneSeqer-medium (Stampede) 5.0.0
- Genotype By Sequencing
- Genotyping By Sequencing Workflow
- GenSel
- gffread-2.2.1
- gffread-2.2.1 convert between GFF3 and GTF2
- Gfold 1.1.1 Count
- Gfold 1.1.1 Difference Expression
- GLM
- gmap_build-2018-03-25
- gmap-2018-03-25
- GNU awk
- GNU grep 3.1-2
- GOanna
- GoSeq
- Graphmap index 0.5.2
- Graphmap index align 0.5.2
- Graphmap owler 0.5.2
- GSNAP 07.23.15
- GSNAP 121212
- GWASSER
- Head
- Heterozygote BAM to Counts
- Heterozygote BAM to Counts, v1.2
- Hisat2-Cuffcompare v1.0
- HISAT2-index-align
- HTProcess_BAMstats-1.0
- HTProcess_CuffDiff-2.2.0
- HTProcess_Cufflinks-2.2.0
- HTProcess_Cufflinks-2.2.1
- HTProcess_Cuffmerge-1
- HTProcess_Cuffmerge-2.2.1
- HTProcess_fastqc-0.1
- HTProcess_fastqc-0.2
- HTProcess_Jellyfish-2.0.0
- HTProcess_Kmergenie-1.0
- HTProcess_Kmergenie-1.7016
- HTProcess_Tophat-2.0.11 (archived)
- HTProcess_Tophat 2.0.13 (archived)
- HTProcess_trimmomatic_0.32
- HTProcess_trimmomatic-0.33
- HTProcess-prepare_directories-and-run_fastqc-0.1
- HTProcess-prepare input directories-0.1
- HTProcess-prepare input directories 0.2
- HTProcess-Tophat-2.0.11 (archived)
- HTProcess-Tophat-2.1.1 (archived)
- HTSeq-count-0.12.4
- HTSeq-count 0.5.4
- HTSeq-count-0.6.1
- Htseq-Count-Merge-0.6.1
- HTSeqQC
- HTSeq-with-BAM-input
- IDBA-UD 1.1.2
- Identification of unique homozygous SNPs in mutant
- IGVtools count
- Index BAM file
- Index BAM--get stats
- Index fasta file (Samtools 1.7 faidx)
- Infernal-1.1.2
- InStruct
- Interlace Paired FASTQ files
- InterProScan_Results_Function
- InterproScan 5.36.75
- IUTA-1.0 in the Discovery Environment
- Join multiple tab-delimited files
- Kallisto
- KBase data upload
- khmer 3.0.0a1 extract paired reads
- khmer 3.0.0a1 filter-abund
- khmer 3.0.0a1 load into counting
- khmer 3.0.0a1 normalize by median
- KOBAS annotate 3.0.3
- KOBAS annotate and identify 3.0.3
- KOBAS identify 3.0.3
- LASTAL-8.69
- LASTDB-8.69
- LD (Tassel4)
- Linux stream editor
- List contents of FAST5 file(s)
- LncTar-1.0
- LTR finder 1.07
- MACS
- MAFFT 7.0.17
- Make new names for fasta sequences
- maker2jbrowse
- maker2zff
- Mapping illumina seq data Part 1
- MaxBin 2.2 in the Discovery Environment
- Medusa-1.6
- Megahit-1.0.6
- Meraculous 2.2.6
- Merge_htseq_count-1.0
- Merge BAM files
- MergeG2P 0.0.2
- Merge SFF files-2.9
- MERRA-AS instM_3d_ana_Np (Analyzed State, Meteorology Instantaneous Monthly)
- MERRA-AS tavg1_2d_lnd_Nx (Land related surface quantities)
- MetaGeneAnnotator-1.0.0
- MetaGeneMark GFF to IGB
- MetaPhyler-SR 0.115
- MetaQUAST-4.0 (denovo based) in DE
- MetaQUAST-4.0 (reference based) in DE
- MetaQUAST-4.3 (denovo based) in DE
- MetaQUAST-4.3 (reference based) in DE
- Mikado
- Miniasm 0.2_r168
- Minimap2_index_align-2.10
- Minimap2_index-2.10
- miRanda 3.3a
- miRDeep2 2.0.0.8
- miRDeep2 2.0.0.8 mapper
- miRDeep2 2.0.0.8 quantifier
- miR-PREFeR
- MLM (Tassel4)
- MLM 4.3.13
- MLMM 0.0.2
- MLM Workflow
- Modify_GFF_coordinates
- Molecular Dating with Penalized Likelihood
- mpileup
- MrBayes_mpi_basic-3.2.3
- MrBayes on CyVerse UK
- Mugsy 1.2.3
- MUSCLE
- MUSCLE-3.8.31 on Stampede
- Mutant Identification 1
- mutant interval identification
- nanofilt 2.5.0
- Nanopolish-call-methylation-0.10.2
- Nanopolish-eventalign-0.10.2
- Nanopolish-eventalign-0.7.1
- Nanopolish-extract-0.10.2
- Nanopolish-extract-0.8.1
- Nanopolish-index-0.10.2
- Nanopolish-index-0.8.1
- Nanopolish-variants-0.10.2
- Nanopolish vcf2fasta 0.10.2
- nanoqc 0.91
- NCBI GenBank Import
- NCBI SRA Import
- NCBI SRA Import 1.2
- NCBI SRA Submission - BioProject Creation
- NCBI SRA Submission - BioProject Update
- NCBI SRA Submission Report Retrieval
- NCBI SRA Toolkit fastq-dump 2.1.9
- NCBI SRA Toolkit fastq-dump 2.3.4
- NCBI SRA Toolkit fastq-dump 2.8.1
- NCBI SRA to Solid Format (abi-dump)
- Newbler
- Newbler 2.6.0
- NGMLR 0.2.7
- Ninja
- non-unique filter
- Normalize By Median
- NPUTE-0.0.1
- NumericalTransform 4.3.14
- Numeric Evaluation of a Data Column
- Oases 0.2.08
- Ontologizer
- OposSOM-2.0.1-biomart
- OrthoFinder 2.5.2
- OrthoMCL v1.4
- PAGE
- PAML