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core-snp-filter
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public |
Filtering sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment.
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2024-12-12 |
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ucsc-mafsinregion
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public |
Extract MAFS in a genomic region
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2024-12-12 |
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ucsc-farc
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public |
Reverse complement a FA file
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2024-12-12 |
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ucsc-maftosnpbed
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public |
finds SNPs in MAF and builds a bed with their functional consequence
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2024-12-12 |
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ucsc-maskoutfa
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public |
Produce a masked .fa file given an unmasked .fa and
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2024-12-12 |
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ucsc-gff3topsl
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public |
convert a GFF3 CIGAR file to a PSL file
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2024-12-12 |
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smudgeplot_rn
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public |
Inference of ploidy and heterozygosity structure using whole genome sequencing data. Fork of Kamil S. Jarons Smudgeplot.
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2024-12-12 |
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pgenlib
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public |
Python wrapper for pgenlib's basic reader and writer.
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2024-12-12 |
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bayestyper
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public |
A method for variant graph genotyping based on exact alignment of k-mers
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2024-12-12 |
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est-sfs
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public |
est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML).
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2024-12-12 |
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links
|
public |
Long Interval Nucleotide K-mer Scaffolder
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2024-12-12 |
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r-momf
|
public |
The package can fit single RNA-seq data set(SOMF) and multiple RNA-seq data sets (MOMF).
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2024-12-12 |
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derna
|
public |
RNA sequence design for a target protein sequence.
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2024-12-12 |
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gum
|
public |
A header-only library for representation of sequence graphs
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2024-12-12 |
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mbg
|
public |
Minimizer based sparse de Bruijn graph constructor
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2024-12-12 |
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daligner
|
public |
DALIGNER: Find all significant local alignments between reads
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2024-12-12 |
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riblast
|
public |
RIblast is ultrafast RNA-RNA interaction prediction software.
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2024-12-12 |
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carnac-lr
|
public |
Clustering coefficient-based Acquisition of RNA Communities in Long Read
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2024-12-12 |
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repaq
|
public |
A fast lossless FASTQ compressor with ultra-high compression ratio
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2024-12-12 |
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blockbuster
|
public |
Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.
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2024-12-12 |
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r-seurat-disk
|
public |
The h5Seurat file format is specifically designed for the storage and analysis of multi-modal single-cell and spatially-resolved expression experiments, for example, from CITE-seq or 10X Visium technologies. It holds all molecular information and associated metadata, including (for example) nearest-neighbor graphs, dimensional reduction information, spatial coordinates and image data, and cluster labels. We also support rapid and on-disk conversion between h5Seurat and AnnData objects, with the goal of enhancing interoperability between Seurat and Scanpy.
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2024-12-12 |
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gtfsort
|
public |
A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm.
|
2024-12-12 |
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ucsc-transmappsltogenepred
|
public |
convert PSL alignments of mRNAs to gene annotations.
|
2024-12-12 |
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porechop_abi
|
public |
Adapter inferrence and removal of Oxford Nanopore reads
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2024-12-12 |
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wtdbg
|
public |
Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
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2024-12-12 |
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pbjasmine
|
public |
jasmine
|
2024-12-12 |
|
survivor
|
public |
Toolset for SV simulation, comparison and filtering
|
2024-12-12 |
|
genion
|
public |
Characterizing gene fusions using long transcriptomics reads
|
2024-12-12 |
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netcdf-metadata-info
|
public |
Metadata information from netcdf file for Galaxy use.
|
2024-12-12 |
|
haplink
|
public |
Viral haplotype calling via linkage disequilibrium
|
2024-12-12 |
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fingerprintscan
|
public |
Search against FingerPRINTScan with a protein query sequence to identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.
|
2024-12-12 |
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sabre
|
public |
A barcode demultiplexing and trimming tool for FastQ files
|
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 |
|
cmph
|
public |
No Summary
|
2024-12-12 |
|
merfishtools
|
public |
MERFISHtools implement a Bayesian framework for accurately predicting gene or transcript expression from MERFISH data. On top, differential expression analysis can be performed for two or multiple conditions, including credible intervals for fold change and coefficient of variation, and controlling the expected false discovery rate.
|
2024-12-12 |
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bgt
|
public |
Flexible genotype query among 30,000+ samples whole-genome.
|
2024-12-12 |
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classpro
|
public |
A K-mer classifier for HiFi reads .
|
2024-12-12 |
|
pysais
|
public |
Suffix array computation with induced sorting algorithm.
|
2024-12-12 |
|
pb-falconc
|
public |
C utilities for PacBio assembly (pbipa etc.)
|
2024-12-12 |
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ucsc-bigmaftomaf
|
public |
convert bigMaf to maf file
|
2024-12-12 |
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ucsc-bigbednameditems
|
public |
Extract item of given name from bigBed
|
2024-12-12 |
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conus
|
public |
CONUS is an implementation of simple stochastic context-free grammars for RNA secondary structure analysis.CONUS developed for exploring the consequences of different single sequence SCFG designs in predicting RNA secondary structure.
|
2024-12-12 |
|
spoa
|
public |
SIMD partial order alignment tool/library
|
2024-12-12 |
|
dazz_db
|
public |
DAZZ_DB: The Dazzler Data Base
|
2024-12-12 |
|
biobloomtools
|
public |
Building Bloom filters and using them for categorizing sequences
|
2024-12-12 |
|
coverageanomalyscanner
|
public |
Application to find local anomalies in read coverage and to predict putative SV events.
|
2024-12-12 |
|
smashpp
|
public |
A fast tool to find and visualize rearrangements in DNA sequences
|
2024-12-12 |
|
ucsc-bigwiginfo
|
public |
Print out information about bigWig file.
|
2024-12-12 |
|
get_fasta_info
|
public |
get_FAST{A,Q}_info - Get fast info on fasta and fastq files
|
2024-12-12 |
