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r-seurat-data
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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
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public |
Fast implementation of the neighbour-joining phylogenetic inference method
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2024-12-14 |
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ucsc-qactoqa
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public |
convert from compressed to uncompressed
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2024-12-14 |
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ropebwt2
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public |
Incremental construction of FM-index for DNA sequences
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2024-12-14 |
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enano
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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
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public |
DNA sequence utilities
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2024-12-14 |
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newick_utils
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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
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public |
Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments.
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2024-12-14 |
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mapad
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public |
An aDNA aware short-read mapper
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2024-12-14 |
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skani
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public |
skani is a fast and robust tool for calculating ANI between metagenome assembled genomes and contigs.
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2024-12-14 |
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mapping-iterative-assembler
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public |
Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria.
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2024-12-14 |
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r-intego
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public |
An unsupervised gene clustering algorithm based on the integration of external biological knowledge, such as Gene Ontology annotations, into expression data.
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2024-12-14 |
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htslib
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public |
C library for high-throughput sequencing data formats.
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2024-12-14 |
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bbknn
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public |
Batch balanced KNN
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2024-12-14 |
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ucsc-genepredtoprot
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public |
create protein sequences by translating gene annotations
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2024-12-14 |
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wgsim
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public |
No Summary
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2024-12-14 |
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deepchopper-cli
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public |
A CLI for Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing.
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2024-12-14 |
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atac
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public |
No Summary
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2024-12-14 |
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table2asn
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public |
table2asn is a command-line program that creates sequence records for submission to GenBank - replaces tbl2asn.
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2024-12-14 |
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slow5tools
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public |
Toolkit for S/bLOW5 format
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2024-12-14 |
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ucsc-bedpileups
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public |
Find (exact) overlaps if any in bed input
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2024-12-14 |
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cansam
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public |
C++ binding for SAM/BAM files
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2024-12-14 |
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perl-time-hires
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public |
High resolution alarm, sleep, gettimeofday, interval timers
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2024-12-14 |
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bowtie
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public |
An ultrafast memory-efficient short read aligner
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2024-12-14 |
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perl-digest-sha1
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public |
Perl interface to the SHA-1 algorithm
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2024-12-14 |
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ucsc-fatrans
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public |
Translate DNA .fa file to peptide
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2024-12-14 |
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contrafold
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public |
CONditional TRAining for RNA Secondary Structure Prediction
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2024-12-14 |
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ucsc-checkagpandfa
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public |
takes a .agp file and .fa file and ensures that they are in synch
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2024-12-14 |
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perl-unicode-normalize
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public |
Unicode Normalization Forms
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2024-12-14 |
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ucsc-mafmefirst
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public |
Move component to top if it is one of the named ones.
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2024-12-14 |
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meta-neuro
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public |
Medial Tractography Analysis (MeTA)
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2024-12-14 |
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fasttree
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public |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
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2024-12-14 |
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ucsc-chainantirepeat
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public |
Get rid of chains that are primarily the results of repeats and degenerate DNA
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2024-12-14 |
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crass
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public |
Crass (The CRISPR Assembler) is a program that searches through raw metagenomic reads for Clustered Regularly Interspersed Short Palindromic Repeats
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2024-12-14 |
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ucsc-hgsqldump
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public |
Execute mysqldump using passwords from .hg.conf
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2024-12-14 |
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perl-unicode-map
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public |
Map charsets from and to UTF-16 unicode
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2024-12-14 |
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ucsc-mafspecieslist
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public |
Scan maf and output all species used in it.
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2024-12-14 |
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ucsc-pslrc
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public |
reverse-complement psl
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2024-12-14 |
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meraculous
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public |
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.
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2024-12-14 |
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hisat2
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public |
Graph-based alignment of next generation sequencing reads to a population of genomes.
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2024-12-14 |
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ucsc-bedgraphpack
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public |
Pack together adjacent records representing same value.
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2024-12-14 |
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perl-convert-binary-c
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public |
Binary Data Conversion using C Types
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2024-12-14 |
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sketchy
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public |
Real-time lineage hashing and genotyping of bacterial pathogens
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2024-12-14 |
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parafly
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public |
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
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2024-12-14 |
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phyml
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public |
Phylogenetic estimation using (Maximum) Likelihood
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2024-12-14 |
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ucsc-maftoaxt
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public |
Convert from maf to axt format
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2024-12-14 |
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irfinder
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public |
Intron Retention Finder
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2024-12-14 |
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ucsc-genepredtobed
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public |
Convert from genePred to bed format. Does not yet handle genePredExt
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2024-12-14 |
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tntblast
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public |
Searching DNA/RNA sequence databases with PCR and/or probe queries
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2024-12-14 |
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ucsc-chaincleaner
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public |
Remove chain-breaking alignments from chains that break nested chains.
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2024-12-14 |
