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savvy
|
public |
Interface to various variant calling formats.
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2024-12-14 |
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r-grbase
|
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.
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2024-12-14 |
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ucsc-autodtd
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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.
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2024-12-14 |
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csblast
|
public |
Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.
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2024-12-14 |
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yacrd
|
public |
Yet Another Chimeric Read Detector, with long-read mapper result as input.
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2024-12-14 |
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dupsifter
|
public |
A tool for PCR duplicate marking of WGBS (and WGS) data.
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2024-12-14 |
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ucsc-fafrag
|
public |
Extract a piece of DNA from a .fa file.
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2024-12-14 |
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circminer
|
public |
Sensitive and fast computational tool for detecting circular RNAs (circRNAs) from RNA-Seq data.
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2024-12-14 |
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ucsc-twobitdup
|
public |
check to see if a twobit file has any identical sequences in it
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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
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2024-12-14 |
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soapec
|
public |
a correction tool for SOAPdenovo
|
2024-12-14 |
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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.
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2024-12-14 |
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quicktree
|
public |
Fast implementation of the neighbour-joining phylogenetic inference method
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2024-12-14 |
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ucsc-qactoqa
|
public |
convert from compressed to uncompressed
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2024-12-14 |
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ropebwt2
|
public |
Incremental construction of FM-index for DNA sequences
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2024-12-14 |
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enano
|
public |
ENANO is a FASTQ compression tool especially designed for nanopore sequencing FASTQ files.
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2024-12-14 |
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seqfu
|
public |
DNA sequence utilities
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2024-12-14 |
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newick_utils
|
public |
The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).
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2024-12-14 |
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sgdemux
|
public |
Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.
|
2024-12-14 |
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mapad
|
public |
An aDNA aware short-read mapper
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2024-12-14 |
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skani
|
public |
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
|
2024-12-14 |
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mapping-iterative-assembler
|
public |
Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria.
|
2024-12-14 |
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r-intego
|
public |
An unsupervised gene clustering algorithm based on the integration of external biological knowledge, such as Gene Ontology annotations, into expression data.
|
2024-12-14 |
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htslib
|
public |
C library for high-throughput sequencing data formats.
|
2024-12-14 |
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bbknn
|
public |
Batch balanced KNN
|
2024-12-14 |
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ucsc-genepredtoprot
|
public |
create protein sequences by translating gene annotations
|
2024-12-14 |
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wgsim
|
public |
No Summary
|
2024-12-14 |
|
deepchopper-cli
|
public |
A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.
|
2024-12-14 |
|
atac
|
public |
No Summary
|
2024-12-14 |
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table2asn
|
public |
table2asn is a command-line program that creates sequence records for submission to GenBank - replaces tbl2asn.
|
2024-12-14 |
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slow5tools
|
public |
Toolkit for S/bLOW5 format
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2024-12-14 |
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ucsc-bedpileups
|
public |
Find (exact) overlaps if any in bed input
|
2024-12-14 |
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cansam
|
public |
C++ binding for SAM/BAM files
|
2024-12-14 |
|
perl-time-hires
|
public |
High resolution alarm, sleep, gettimeofday, interval timers
|
2024-12-14 |
|
bowtie
|
public |
An ultrafast memory-efficient short read aligner
|
2024-12-14 |
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perl-digest-sha1
|
public |
Perl interface to the SHA-1 algorithm
|
2024-12-14 |
|
ucsc-fatrans
|
public |
Translate DNA .fa file to peptide
|
2024-12-14 |
|
contrafold
|
public |
CONditional TRAining for RNA Secondary Structure Prediction
|
2024-12-14 |
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ucsc-checkagpandfa
|
public |
takes a .agp file and .fa file and ensures that they are in synch
|
2024-12-14 |
|
perl-unicode-normalize
|
public |
Unicode Normalization Forms
|
2024-12-14 |
|
ucsc-mafmefirst
|
public |
Move component to top if it is one of the named ones.
|
2024-12-14 |
|
meta-neuro
|
public |
Medial Tractography Analysis (MeTA)
|
2024-12-14 |
|
fasttree
|
public |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
|
2024-12-14 |
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ucsc-chainantirepeat
|
public |
Get rid of chains that are primarily the results of repeats and degenerate DNA
|
2024-12-14 |
|
crass
|
public |
Crass (The CRISPR Assembler) is a program that searches through raw metagenomic reads for Clustered Regularly Interspersed Short Palindromic Repeats
|
2024-12-14 |
|
ucsc-hgsqldump
|
public |
Execute mysqldump using passwords from .hg.conf
|
2024-12-14 |
|
perl-unicode-map
|
public |
Map charsets from and to UTF-16 unicode
|
2024-12-14 |
