|
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 |
|
r-biodb
|
public |
An R package for connecting to chemical and biological databases.
|
2024-12-12 |
|
gffcompare
|
public |
GffCompare by Geo Pertea
|
2024-12-12 |
|
boutroslabplottinggeneral
|
public |
No Summary
|
2024-12-12 |
|
ucsc-fastqtofa
|
public |
Convert from fastq to fasta format.
|
2024-12-12 |
|
ucsc-hgloadmaf
|
public |
Load a maf file index into the database
|
2024-12-12 |
|
ucsc-mafaddqrows
|
public |
Add quality data to a maf
|
2024-12-12 |
|
ucsc-mafsinregion
|
public |
Extract MAFS in a genomic region
|
2024-12-12 |
|
ucsc-farc
|
public |
Reverse complement a FA file
|
2024-12-12 |
|
ucsc-maftosnpbed
|
public |
finds SNPs in MAF and builds a bed with their functional consequence
|
2024-12-12 |
|
ucsc-maskoutfa
|
public |
Produce a masked .fa file given an unmasked .fa and
|
2024-12-12 |
|
ucsc-gff3topsl
|
public |
convert a GFF3 CIGAR file to a PSL file
|
2024-12-12 |
|
links
|
public |
Long Interval Nucleotide K-mer Scaffolder
|
2024-12-12 |
|
daligner
|
public |
DALIGNER: Find all significant local alignments between reads
|
2024-12-12 |
|
blockbuster
|
public |
Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.
|
2024-12-12 |
|
regtools
|
public |
Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
|
2024-12-12 |
|
ucsc-transmappsltogenepred
|
public |
convert PSL alignments of mRNAs to gene annotations.
|
2024-12-12 |
|
wtdbg
|
public |
Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
|
2024-12-12 |
|
survivor
|
public |
Toolset for SV simulation, comparison and filtering
|
2024-12-12 |
|
netcdf-metadata-info
|
public |
Metadata information from netcdf file for Galaxy use.
|
2024-12-12 |
|
bwa
|
public |
The BWA read mapper.
|
2024-12-12 |
|
fermi
|
public |
A WGS de novo assembler based on the FMD-index for large genomes
|
2024-12-12 |
