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ucsc-maffrags
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public |
Collect MAFs from regions specified in a 6 column bed file
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2024-12-14 |
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perl-want
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public |
No Summary
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2024-12-14 |
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scrm
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public |
A coalescent simulator for genome-scale sequences
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2024-12-14 |
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python-msgpack
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public |
It's like JSON. But fast and small.
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2024-12-14 |
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rapifilt
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public |
RAPIFILT:RAPId FILTer is a quality control of DNA sequences
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2024-12-14 |
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ucsc-netclass
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public |
Add classification info to net
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2024-12-14 |
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perl-dbd-sqlite
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public |
Self Contained RDBMS in a DBI Driver
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2024-12-14 |
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ucsc-qactowig
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public |
convert from compressed quality score format to wiggle format.
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2024-12-14 |
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nextdenovo
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public |
String graph-based de novo assembler for long reads (CLR, HiFi and ONT)
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2024-12-14 |
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bs_call
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public |
DNA methylation and variant Caller for Bisulfite Sequencing Data.
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2024-12-14 |
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ucsc-autoxml
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public |
Generate structures code and parser for XML file from DTD-like spec
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2024-12-14 |
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psdm
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public |
Compute a pairwise SNP distance matrix from one or two alignment(s)
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2024-12-14 |
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strobemap
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public |
Efficient string matching using strobemers
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2024-12-14 |
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kyototycoon
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public |
a lightweight network server on top of the Kyoto Cabinet key-value database, built for high-performance and concurrency
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2024-12-14 |
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ucsc-autosql
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public |
create SQL and C code for permanently storing
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2024-12-14 |
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r-scdc
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public |
SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.
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2024-12-14 |
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ucsc-twobitinfo
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public |
Get information about sequences in a .2bit file.
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2024-12-14 |
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ucsc-tdbquery
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public |
Query the trackDb system using SQL syntax.
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2024-12-14 |
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r-sgtr
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public |
Visualize population genomics analyses results in R.
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2024-12-14 |
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sword
|
public |
SWORD - a highly efficient protein database search
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2024-12-14 |
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r-tcr
|
public |
Platform for the advanced analysis of T cell receptor and Immunoglobulin repertoires data and visualisation of the analysis results.
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2024-12-14 |
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clonalframeml
|
public |
Efficient inferencing of recombination in bacterial genomes
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2024-12-14 |
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perl-scalar-util-numeric
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public |
numeric tests for perl scalars
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2024-12-14 |
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ucsc-dbtrash
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public |
drop tables from a database older than specified N hours
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2024-12-14 |
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msalign2
|
public |
Aligns 2 CE-MS or LC-MS datasets using accurate mass information.
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2024-12-14 |
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smafa
|
public |
smafa is a tool for querying and clustering pre-aligned small pre-aligned sequences.
|
2024-12-14 |
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srprism
|
public |
SRPRISM - Short Read Alignment Tool
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2024-12-14 |
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cloudspades
|
public |
A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging).
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2024-12-14 |
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orna
|
public |
In silico read normalization
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2024-12-14 |
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slclust
|
public |
A utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.
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2024-12-14 |
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mapseq
|
public |
Open source metagenomic 16S/18S read classifier enabling comparative metagenomics.
|
2024-12-14 |
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ushuffle
|
public |
uShuffle---a useful tool for shuffling biological sequences while preserving the k-let counts
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2024-12-14 |
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savvy
|
public |
Interface to various variant calling formats.
|
2024-12-14 |
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r-grbase
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public |
The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details. NOTICE 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.
|
2024-12-14 |
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ucsc-autodtd
|
public |
Give this a XML document to look at and it will come up with a DTD
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2024-12-14 |
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vcf2parquet
|
public |
Convert a vcf in parquet.
|
2024-12-14 |
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csblast
|
public |
Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.
|
2024-12-14 |
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yacrd
|
public |
Yet Another Chimeric Read Detector, with long-read mapper result as input.
|
2024-12-14 |
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dupsifter
|
public |
A tool for PCR duplicate marking of WGBS (and WGS) data.
|
2024-12-14 |
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ucsc-fafrag
|
public |
Extract a piece of DNA from a .fa file.
|
2024-12-14 |
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circminer
|
public |
Sensitive and fast computational tool for detecting circular RNAs (circRNAs) from RNA-Seq data.
|
2024-12-14 |
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ucsc-twobitdup
|
public |
check to see if a twobit file has any identical sequences in it
|
2024-12-14 |
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kallisto
|
public |
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
|
2024-12-14 |
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pstools
|
public |
Toolkit for fully phased sequences
|
2024-12-14 |
|
soapec
|
public |
a correction tool for SOAPdenovo
|
2024-12-14 |
|
kmc
|
public |
Tools for efficient k-mer counting and filtering of reads based on k-mer content.
|
2024-12-14 |
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r-seurat-data
|
public |
Single cell RNA sequencing datasets can be large, consisting of matrices that contain expression data for several thousand features across several thousand cells. This package is designed to easily install, manage, and learn about various single-cell datasets, provided Seurat objects and distributed as independent packages.
|
2024-12-14 |
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ucsc-qactoqa
|
public |
convert from compressed to uncompressed
|
2024-12-14 |
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ropebwt2
|
public |
Incremental construction of FM-index for DNA sequences
|
2024-12-14 |
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enano
|
public |
ENANO is a FASTQ compression tool especially designed for nanopore sequencing FASTQ files.
|
2024-12-14 |
