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ucsc-fasomerecords
|
public |
Extract multiple fa records
|
2024-12-12 |
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zagros
|
public |
No Summary
|
2024-12-12 |
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perl-findbin-real
|
public |
Locates the full path to the script bin directory to allow the use of paths relative to the bin directory.
|
2024-12-12 |
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perl-list-someutils
|
public |
Provide the stuff missing in List::Util
|
2024-12-12 |
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bloocoo
|
public |
Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. As an example, it can correct whole human genome re-sequencing reads at 70 x coverage with less than 4GB of memory.
|
2024-12-12 |
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cofold
|
public |
An RNA secondary structure prediction method that takes co-transcriptional folding into account.
|
2024-12-12 |
|
nmrglue
|
public |
A module for working with NMR data in Python
|
2024-12-12 |
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trf
|
public |
Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
|
2024-12-12 |
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ucsc-countchars
|
public |
Count the number of occurrences of a particular char
|
2024-12-12 |
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vcftools
|
public |
A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
|
2024-12-12 |
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seqtk
|
public |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
|
2024-12-12 |
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ucsc-wordline
|
public |
chop up words by white space and output them with one
|
2024-12-12 |
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ucsc-netsplit
|
public |
Split a genome net file into chromosome net files
|
2024-12-12 |
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ucsc-qacagplift
|
public |
Use AGP to combine per-scaffold qac into per-chrom qac.
|
2024-12-12 |
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bamhash
|
public |
No Summary
|
2024-12-12 |
|
ucsc-faalign
|
public |
Align two fasta files
|
2024-12-12 |
|
evidencemodeler
|
public |
Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures
|
2024-12-12 |
|
assemblyutility
|
public |
No Summary
|
2024-12-12 |
|
python-hyphy-python
|
public |
HyPhy package interface library
|
2024-12-12 |
|
fastsimbac
|
public |
Models bacterial recombination
|
2024-12-12 |
|
ucsc-catdir
|
public |
concatenate files in directory to stdout.
|
2024-12-12 |
|
ucsc-fatotab
|
public |
convert fa file to tab separated file
|
2024-12-12 |
|
ucsc-getrnapred
|
public |
Get virtual RNA for gene predictions
|
2024-12-12 |
|
r-loom
|
public |
An interface for the single-cell RNAseq-oriented loom format. Loom files are an HDF5-based format for storing and interacting with large single-cell RNAseq datasets. loomR provides an interface for working with loom files in a loom-specific way; we provide routines for validating loom files, iterating with chunks through data within the loom file, and provide a platform for other packages to build support for loom files.
|
2024-12-12 |
|
ucsc-mafsplit
|
public |
Split multiple alignment files
|
2024-12-12 |
|
snp-dists
|
public |
Convert a FASTA alignment to SNP distance matrix
|
2024-12-12 |
|
aragorn
|
public |
ARAGORN, tRNA (and tmRNA) detection
|
2024-12-12 |
|
mappy
|
public |
Minimap2 Python binding
|
2024-12-12 |
|
ucsc-pslmap
|
public |
map PSLs alignments to new targets using alignments of
|
2024-12-12 |
|
ucsc-psltobed
|
public |
transform a psl format file to a bed format file.
|
2024-12-12 |
|
r-soap-nmr
|
public |
No Summary
|
2024-12-12 |
|
ucsc-crtreeindexbed
|
public |
Create an index for a bed file.
|
2024-12-12 |
|
mlrho
|
public |
Takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, , the sequencing error , the zygosity correlation, and the population recombination rate.
|
2024-12-12 |
|
ucsc-bedgeneparts
|
public |
Given a bed, spit out promoter, first exon, or all introns.
|
2024-12-12 |
|
seq-gen
|
public |
Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.
|
2024-12-12 |
|
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.
|
2024-12-12 |
|
tidyp
|
public |
Program for cleaning up and validating HTML
|
2024-12-12 |
|
ucsc-psltopslx
|
public |
Convert from psl to pslx format, which includes sequences
|
2024-12-12 |
|
perl-heap-simple-xs
|
public |
No Summary
|
2024-12-12 |
|
ucsc-gaptolift
|
public |
create lift file from gap table(s)
|
2024-12-12 |
|
adapterremoval
|
public |
The AdapterRemoval v2 tool for merging and clipping reads.
|
2024-12-12 |
|
ucsc-bigwigcat
|
public |
merge non-overlapping bigWig files
|
2024-12-12 |
|
ucsc-pslselect
|
public |
select records from a PSL file.
|
2024-12-12 |
|
ucsc-bigwigmerge
|
public |
Merge together multiple bigWigs into a single output bedGraph.
|
2024-12-12 |
|
ucsc-pslmrnacover
|
public |
Make histogram of coverage percentage of mRNA in psl.
|
2024-12-12 |
|
ucsc-mafspeciessubset
|
public |
Extract a maf that just has a subset of species.
|
2024-12-12 |
|
fastq-and-furious
|
public |
Fast handling of FASTQ files
|
2024-12-12 |
|
ucsc-hgloadnet
|
public |
Load a generic net file into database
|
2024-12-12 |
|
tantan
|
public |
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
|
2024-12-12 |
|
ucsc-hgloadout
|
public |
load RepeatMasker .out files into database
|
2024-12-12 |
