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bioconda / packages

Package Name Access Summary Updated
ucsc-hgsqldump public Execute mysqldump using passwords from .hg.conf. 2025-06-29
ucsc-hgloadmaf public Load a maf file index into the database. 2025-06-29
ucsc-getrna public Get mrna for GenBank or RefSeq sequences found in a database. 2025-06-29
ucsc-texthistogram public Make a histogram in ascii. 2025-06-29
ucsc-gff3topsl public Convert a GFF3 CIGAR file to a PSL file. 2025-06-29
ucsc-maftobigmaf public Put ucsc standard maf file into bigMaf format. 2025-06-29
ucsc-mrnatogene public Convert PSL alignments of mRNAs to gene annotations. 2025-06-29
ucsc-genepredtomafframes public Create mafFrames tables from a genePreds. 2025-06-29
ucsc-genepredsinglecover public Create single-coverage genePred files. 2025-06-29
ucsc-pslswap public Swap target and query in psls. 2025-06-28
ucsc-pslmrnacover public Make histogram of coverage percentage of mRNA in psl. 2025-06-28
ucsc-pslcat public Concatenate psl files. 2025-06-28
ucsc-pslreps public Analyze repeats and generate genome-wide best alignments from a sorted set of local alignments. 2025-06-28
ucsc-pslscore public Calculate web blat score from psl files. 2025-06-28
ucsc-pslselect public Select records from a PSL file. 2025-06-28
ucsc-pslxtofa public Convert pslx (with sequence) to fasta file. 2025-06-28
ucsc-pslfilter public Filter out psl file. 2025-06-28
ucsc-psldropoverlap public Deletes all overlapping self alignments. 2025-06-28
ucsc-parafetch public Try to fetch url with multiple connections. 2025-06-28
ucsc-psltopslx public Convert from psl to pslx format, which includes sequences. 2025-06-28
ucsc-pslpartition public Split PSL files into non-overlapping sets. 2025-06-28
ucsc-pslrecalcmatch public Recalculate match, mismatch, repMatch columns in psl file. 2025-06-28
ucsc-pslpretty public Convert PSL to human-readable output. 2025-06-28
ucsc-positionaltblcheck public Check that positional tables are sorted. 2025-06-28
ucsc-pslmappostchain public Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues. 2025-06-28

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