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abawaca
|
public |
No Summary
|
2024-12-14 |
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mea
|
public |
Mea was developed as part of the lab class "Bioinformatik von RNA- und Proteinstrukturen (Praktikum, Modul 10-202-2208)". The package predicts maximum expected accuracy (MEA) RNA secondary structures from dot plots of RNAs while correcting the score in dependence of base pair span. Furthermore, it provides tools to evaluate predictions and optimize parameters.
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2024-12-14 |
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ghostz
|
public |
GHOSTZ is a highly efficient remote homologue detection tool
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2024-12-14 |
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rfmix
|
public |
RFMix implements a fast discriminative approach to modeling ancestry along an admixed chromosome given observed haplotype sequences of known or inferred ancestry.
|
2024-12-14 |
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micro_razers
|
public |
MicroRazerS - Rapid Alignment of Small RNA Reads
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2024-12-14 |
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simka
|
public |
Simka and simkaMin are de novo comparative metagenomics tools. Simka represents each dataset as a k-mer spectrum and computes several classical ecological distances between them. SimkaMin outputs approximate (but very similar) results by subsampling the kmer space and requires much less computational resources.
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2024-12-14 |
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ucsc-mrnatogene
|
public |
convert PSL alignments of mRNAs to gene annotations
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2024-12-14 |
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pbsim
|
public |
No Summary
|
2024-12-14 |
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gadem
|
public |
A Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an EM Algorithm for Motif Discovery
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2024-12-14 |
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ucsc-fasplit
|
public |
Split an fa file into several files.
|
2024-12-14 |
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ucsc-validatemanifest
|
public |
Validates the ENCODE3 manifest.txt file.
|
2024-12-14 |
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ucsc-chromgraphfrombin
|
public |
Convert chromGraph binary to ascii format.
|
2024-12-14 |
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dascrubber
|
public |
Alignment-based Scrubbing pipeline
|
2024-12-14 |
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ucsc-fafiltern
|
public |
Get rid of sequences with too many N's
|
2024-12-14 |
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ucsc-paranodestop
|
public |
Shut down parasol node daemons on a list of machines
|
2024-12-14 |
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codingquarry
|
public |
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
|
2024-12-14 |
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fastool
|
public |
A simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them.
|
2024-12-14 |
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fastq-scan
|
public |
FASTQ summary statistics in JSON format
|
2024-12-14 |
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ucsc-pslxtofa
|
public |
convert pslx (with sequence) to fasta file
|
2024-12-14 |
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kfoots
|
public |
The package provides methods for fitting multivariate count data with a mixture model or a hidden markov model. Each mixture component is a negative multivariate random variable and an EM algorithm is used to maximize the likelihood.
|
2024-12-14 |
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gdc
|
public |
Utility designed for compression of genome collections from the same species.
|
2024-12-14 |
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ucsc-maffrags
|
public |
Collect MAFs from regions specified in a 6 column bed file
|
2024-12-14 |
|
perl-want
|
public |
No Summary
|
2024-12-14 |
|
scrm
|
public |
A coalescent simulator for genome-scale sequences
|
2024-12-14 |
|
python-msgpack
|
public |
It's like JSON. But fast and small.
|
2024-12-14 |
|
ucsc-netclass
|
public |
Add classification info to net
|
2024-12-14 |
|
perl-dbd-sqlite
|
public |
Self Contained RDBMS in a DBI Driver
|
2024-12-14 |
|
ucsc-qactowig
|
public |
convert from compressed quality score format to wiggle format.
|
2024-12-14 |
|
bs_call
|
public |
DNA methylation and variant Caller for Bisulfite Sequencing Data.
|
2024-12-14 |
|
ucsc-autoxml
|
public |
Generate structures code and parser for XML file from DTD-like spec
|
2024-12-14 |
|
ucsc-autosql
|
public |
create SQL and C code for permanently storing
|
2024-12-14 |
|
ucsc-twobitinfo
|
public |
Get information about sequences in a .2bit file.
|
2024-12-14 |
|
kma
|
public |
KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
|
2024-12-14 |
|
ucsc-tdbquery
|
public |
Query the trackDb system using SQL syntax.
|
2024-12-14 |
|
clonalframeml
|
public |
Efficient inferencing of recombination in bacterial genomes
|
2024-12-14 |
|
perl-scalar-util-numeric
|
public |
numeric tests for perl scalars
|
2024-12-14 |
|
ucsc-dbtrash
|
public |
drop tables from a database older than specified N hours
|
2024-12-14 |
|
msalign2
|
public |
Aligns 2 CE-MS or LC-MS datasets using accurate mass information.
|
2024-12-14 |
|
randfold
|
public |
No Summary
|
2024-12-14 |
|
srprism
|
public |
SRPRISM - Short Read Alignment Tool
|
2024-12-14 |
|
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.
|
2024-12-14 |
|
ushuffle
|
public |
uShuffle---a useful tool for shuffling biological sequences while preserving the k-let counts
|
2024-12-14 |
|
ucsc-autodtd
|
public |
Give this a XML document to look at and it will come up with a DTD
|
2024-12-14 |
|
yacrd
|
public |
Yet Another Chimeric Read Detector, with long-read mapper result as input.
|
2024-12-14 |
|
ucsc-fafrag
|
public |
Extract a piece of DNA from a .fa file.
|
2024-12-14 |
|
ucsc-twobitdup
|
public |
check to see if a twobit file has any identical sequences in it
|
2024-12-14 |
|
kallisto
|
public |
Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
|
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 |
|
gseapy
|
public |
Gene Set Enrichment Analysis in Python
|
2024-12-14 |
