| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-gaptolift | public | Create lift file from gap table(s). | 2025-06-26 |
| ucsc-psltochain | public | Convert psl records to chain records. | 2025-06-26 |
| ucsc-psltobed | public | Transform a psl format file to a bed format file. | 2025-06-26 |
| ucsc-pslsort | public | Merge and sort psCluster .psl output files. | 2025-06-26 |
| ucsc-pslsortacc | public | Remove chain-breaking alignments from chains that break nested chains. | 2025-06-26 |
| ucsc-pslstats | public | Collect statistics from a psl file. | 2025-06-26 |
| ucsc-pslpairs | public | Join paired ends in psl alignments. | 2025-06-26 |
| ucsc-qactowig | public | Convert from compressed quality score format to wiggle format. | 2025-06-26 |
| ucsc-ixixx | public | Create indices for simple line-oriented file of format. | 2025-06-26 |
| ucsc-bigwiginfo | public | Print out information about bigWig file. | 2025-06-26 |
| ucsc-bigwigtobedgraph | public | Convert from bigWig to bedGraph format. | 2025-06-26 |
| ucsc-gff3togenepred | public | Convert a GFF3 file to a genePred file. | 2025-06-26 |
| ucsc-pslcheck | public | Validate PSL files. | 2025-06-25 |
| ucsc-nibfrag | public | Extract part of a nib file as .fa (all bases/gaps lower case by default). | 2025-06-25 |
| ucsc-bigwigtowig | public | Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones. | 2025-06-25 |
| celltypist | public | A tool for semi-automatic cell type annotation. | 2025-06-25 |
| poseidon-trident | public | A tool (trident) to work with modular genotype databases formatted using Poseidon. | 2025-06-25 |
| crossmap | public | CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies. | 2025-06-25 |
| ltr_retriever | public | Sensitive and accurate identification of LTR retrotransposons | 2025-06-25 |
| voronota | public | Compute Voronoi diagram vertices for macromolecular structures | 2025-06-25 |
| eklipse | public | eKLIPse is a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements. | 2025-06-25 |
| dendropy | public | A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. | 2025-06-25 |
| beav | public | beav: Bacterial genome and mobile element annotation pipeline | 2025-06-25 |
| demultiplex | public | Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes | 2025-06-25 |
| shortcut | public | ShortCut Small RNA-seq data trimmer and quality control tool | 2025-06-25 |
