| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-matrixclustercolumns | public | Group the columns of a matrix into clusters, and output a matrix with the same number of rows and generally much fewer columns. Combines columns by taking mean. | 2025-06-27 |
| argparse-tui | public | Present your Argparse CLI as a Textual UI (TUI). | 2025-06-27 |
| ucsc-matrixmarkettotsv | public | Convert matrix file from Matrix Market sparse matrix format to tab-separated-values. | 2025-06-26 |
| ucsc-matrixnormalize | public | Normalize a matrix somehow - make it's columns or rows all sum to one or have vector length one. | 2025-06-26 |
| gpatch | public | Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference." | 2025-06-26 |
| nail | public | Profile Hidden Markov Model (pHMM) biological sequence alignment tool | 2025-06-26 |
| vpt-core | public | Core components for the Vizgen Post-processing Tool | 2025-06-26 |
| pydeseq2 | public | A python implementation of DESeq2. | 2025-06-26 |
| masurca | public | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. | 2025-06-26 |
| ucsc-pslsplitontarget | public | Split psl files into one per target. | 2025-06-26 |
| ucsc-bigwigaverageoverbed | public | Compute average score of big wig over each bed, which may have introns. | 2025-06-26 |
| ucsc-bedsort | public | Sort a .bed file by chrom,chromStart. | 2025-06-26 |
| ucsc-xmlcat | public | Concatenate xml files together, stuffing all records inside a single outer tag. | 2025-06-26 |
| ucsc-bigbedsummary | public | Extract summary information from a bigBed file. | 2025-06-26 |
| ucsc-bigbedinfo | public | Show information about a bigBed file. | 2025-06-26 |
| ucsc-bedclip | public | Remove lines from bed file that refer to off-chromosome locations. | 2025-06-26 |
| ucsc-pslprottornacoords | public | Convert protein alignments to RNA coordinates. | 2025-06-26 |
| ucsc-pslsplicejunctions | public | Extract splice junctions from a PSL file. | 2025-06-26 |
| fasta_ushuffle | public | a wrapper for uShuffle | 2025-06-26 |
| ucsc-hggcpercent | public | Calculate GC Percentage in 20kb windows. | 2025-06-26 |
| ucsc-genepredtobiggenepred | public | Converts genePred or genePredExt to bigGenePred input (bed format with extra fields). | 2025-06-26 |
| ucsc-genepredcheck | public | Validate genePred files or tables. | 2025-06-26 |
| ucsc-bigbedtobed | public | Convert from bigBed to ascii bed format. | 2025-06-26 |
| binette | public | A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. | 2025-06-26 |
| flexbar | public | Flexible barcode and adapter removal | 2025-06-26 |
