Metatranscriptomics
| Name | Short Description | Language |
| Abricate | Abricate (Seeman, 2016) | C++ |
| AQMM | AQMM (Jiang et al, 2017) | C++ |
| AuPairWise | AuPairWise (Ballouz et al, 2016) | R |
| BAMClean | Clean a BAM file | C++ |
| Ballgown | Ballgown (Fu et al, 2024) | R |
| BamLorenz | Bam-Lorenz (Hoogstrate et al, 2021) | Python |
| BFC | BFC (Zheng et al, 2021) | C++ |
| BiSCaP | BiSCaP (Farrer et al, 2013) | Perl |
| BPSC | BPSC (Vu et al, 2016) | R |
| BreakDancer | BreakDancer (Fan et al, 2014) | C++ |
| BuildFragments | Transcript fragments | R |
| ClipR | ClipR (Hafner et al, 2021) | C++ |
| CHR | Cell cycle gene Homology Region analysis (Muller et al, 2014) | R |
| CMC | CMC (Rupp et al, 2022) | C++ |
| Condetri | Condetri (Smeds et al, 2011) | Perl |
| CORNAS | CORNAS (Low et al, 2016) | R |
| Coverage2Exon | Coverage information for exon | R |
| Delve | Delve (Ranek et al, 2024) | C++ |
| DensityMap | DensityMap (Guizard, 2016) | Perl |
| DEPTH2 | DEPTH2 (Song and Wang, 2022) | R |
| DESeqHetero | Heterogenoues DESeq (Love et al, 2014) | Python |
| DeTiN | DeTiN (Taylor-Weiner et al, 2018) | C++ |
| DirichletMultinomial | Dirichlet-Multinomial Fit (Nowicka et al, 2016) | R |
| DrDisco | DrDisco (Hoogstrate et al, 2021) | C++ |
| EDASeq | EDASeq (Schwartz et al, 2024) | R |
| EmpiricalBayes | Empirical Bayes method for RNA-seq analysis (Ling et al, 2024) | R |
| ExpressionProfile | Profile gene expression levels | R |
| ExtractSSU | Extract small subunit RNA | R |
| FASTP | FASTP (Chen et al, 2018) | C++ |
| FeatureCounts | FeatureCounts (Liao et al, 2014) | C++ |
| GenEXPLV | Generate Expression Profile Levels (Li et al, 2013) | Python |
| Geuvadis | Geuvadis project (Lappalainen et al, 2013) | R |
| GO | Analyze data using Gene Ontology (Thomas et al, 2022) | R |
| GlobalSeq | GlobalSeq (Rauschenberger et al, 2016) | R |
| GNUMAP | GNUMAP alignment (Clement et al, 2010) | C++ |
| GroupKD | Group Knockdown | R |
| HAllA | HAllA (Ghazi et al, 2022) | C++ |
| HISAT2 | HISAT2 (Siren et al, 2014) | C++ |
| HUGO | HUGO gene nomenclature (Braschi et al, 2019) | Python |
| HumanRNAAnnotate | Annotate transcripts using human genome database | R |
| IDemp | IDemp (Zhang et al, 2023) | C++ |
| Junctions | Portions of a BAM file that contain junctions | C++ |
| Kallisto | Kallisto (Bray et al, 2016) alignment | C++ |
| Knots | Fit different knots | R |
| MAST | MAST (Finak et al, 2011) | R |
| MatchGene | Match gene to region | R |
| MergeChromosomes | Merge results from different chromosomes (Collado-Torres et al, 2017) | R |
| Meryl | Meryl (Jain et al, 2020) | C++ |
| MinPath | MinPath (Ye et al, 2009) | Python |
| MitochondriaFilter | Filter out mitochondrial RNA | R |
| MitochondrialRNA | Percentage of mitochondrial transcripts | R |
| MinPath | MinPath (Ye et al, 2009) | Python |
| NGVector | Compute NG-vector | R |
| MIRPREFeR | MIRPREFeR (Lei et al, 2014) | Python |
| PAFScaff | PAFScaff (Edwards et al, 2021) | C++ |
| PBSIM | PBSIM (Ono et al, 2013) | C++ |
| PennSeq | PennSeq (Hu et al, 2014) | Perl |
| Piggy | Piggy (Thorpe et al, 2018) | C++ |
| PISA | PISA (Qi et al, 2022) | C++ |
| PRADA | PRADA (Nellore et al, 2013) | C++ |
| PredictCoverage | Predict gene coverage | R |
| PROPER | PROPER (Wu et al, 2015) | R |
| QC | Quality Control | Python |
| QC3 | Quality Control (Version 3) | Perl |
| QuastRNA | Quast RNA (Bushmanova et al, 2016) | Python |
| Rail | Rail (Neilore et al, 2017) | R |
| RANSAC | RANSAC (Caspi et al, 2017) | Python |
| RBPMotif | RBP motifs | Python |
| RDiff | RDiff (Drewe et al, 2013) | C++ |
| ReadSim | Generate simulated reads (Li et al, 2013) | Python |
| RefSeq | RefSeq target matrix (O'Leary et al, 2016) | Python |
| RegionCoverage | Get region coverage | R |
| RegionMatrix | Identify a region by coverage and count | R |
| RlSim | RlSim (Sipos et al, 2013) | C++ |
| RNAAnnotate | Transcript annotation | R |
| RNAontheBENCH | RNAontheBENCH (Germain et al, 2016) | R |
| RNASeqPower | RNASeqPower (Therneau et al, 2024) | R |
| RSeqNP | RSeqNP (Shi et al, 2015) | R |
| RSTibble | RefSeq data as a tibble | R |
| Sammon | Sammon (Patro et al, 2017) | Python |
| SampleDepth | Sample at a depth and build model | R |
| SCKmer | SCKmer (Ghaddar et al, 2022) | R |
| ScanBamParam | Genomic regions to be considered in feature prediction | R |
| Scoary | Scoary (Brynildsrud et al, 2016) | Python |
| Seq2HLA | Seq2HLA (Boegel et al, 2013) | C++ |
| SGAnalyze | Splice graph analysis | R |
| ShortStack | ShortStack (Axtell et al, 2013) | C++ |
| SignalCalibrate | RNASeq quantification filtering and calibration (Teng et al, 2016) | R |
| SMALT | SMALT alignment (Postingl and Ning, 2020) | C++ |
| Specificity | Specificity (Guo et al, 2015) | R |
| Splatter | Splatter (Zappia et al, 2017) | R |
| SpliceMap | SpliceMap (Au et al, 2010) | C++ |
| SQTL | Splicing QTL Analysis (Yamaguchi et al, 2022) | R |
| Stampy | Stampy (Lunter et al, 2009) | C++ |
| STAR | Spliced Transcripts Alignment to a Reference (Dobin et al, 2009) | C++ |
| Strawberry | Strawberry (Liu et al, 2017) | C++ |
| StringTie | StringTie (Pertea et al, 2015) | C++ |
| Subread | Subread aligner (Lao et al, 2013) | C++ |
| SWIPE | SWIPE (Rognes et al, 2011) | C++ |
| TagCleaner | TagCleaner (Schmeider et al, 2010) | Perl |
| TIGAR | TIGAR (Nagpal et al, 2019) | Python |
| TIGAR | TIGAR (Nagpal et al, 2019) | Python |
| TransComb | TransComb (Liu et al, 2016) | C++ |
| TranscriptFeatures | Obtain transcript features from BAM | R |
| VariantAnalyze | Analysis of splice variants | R |
| VariantCount | Count splice variants | R |
| VariantFreq | Relative usage estimates of variant counts | R |
| VariantPlot | Plot of splice variants | R |
| VariantPred | Splice variant prediction | R |
| Winnowmap | Winnowmap (Jain et al, 2020) | C++ |
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