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fermi
|
public |
A WGS de novo assembler based on the FMD-index for large genomes
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2024-12-12 |
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cmph
|
public |
No Summary
|
2024-12-12 |
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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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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 |
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dazz_db
|
public |
DAZZ_DB: The Dazzler Data Base
|
2024-12-12 |
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ucsc-bigwiginfo
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public |
Print out information about bigWig file.
|
2024-12-12 |
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simwalk2
|
public |
Stochastic Statistical Analysis of Qualitative Traits
|
2024-12-12 |
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fastq-multx
|
public |
Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not.
|
2024-12-12 |
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ucsc-bedsort
|
public |
Sort a .bed file by chrom,chromStart
|
2024-12-12 |
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ucsc-rowstocols
|
public |
Convert rows to columns and vice versa in a text file.
|
2024-12-12 |
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r-sbpiper
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public |
Provides an API for analysing repetitive parameter estimations and simulations of mathematical models. Examples of mathematical models are Ordinary Differential equations (ODEs) or Stochastic Differential Equations (SDEs) models. Among the analyses for parameter estimation 'sbpiper' calculates statistics and generates plots for parameter density, PCA of the best fits, parameter profile likelihood estimations (PLEs), and 2D parameter PLEs. These results can be generated using all or a subset of the best computed parameter sets. Among the analyses for model simulation 'sbpiper' calculates statistics and generates plots for deterministic and stochastic time courses via cartesian and heatmap plots. Plots for the scan of one or two model parameters can also be generated. This package is primarily used by the software 'SBpipe'. Citation: Dalle Pezze P, Le Novère N. SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology. 2017;11:46. <doi:10.1186/s12918-017-0423-3>.
|
2024-12-12 |
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ucsc-overlapselect
|
public |
Select records based on overlapping chromosome ranges. The ranges are specified in the selectFile, with each block specifying a range. Records are copied from the inFile to outFile based on the selection criteria. Selection is based on blocks or exons rather than entire range.
|
2024-12-12 |
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ucsc-spacedtotab
|
public |
Convert fixed width space separated fields to tab separated
|
2024-12-12 |
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ema
|
public |
Fast & accurate alignment of barcoded short-reads
|
2024-12-12 |
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dwgsim
|
public |
Whole Genome Simulator for Next-Generation Sequencing
|
2024-12-12 |
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r-mcpcounter
|
public |
Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression
|
2024-12-12 |
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ucsc-xmltosql
|
public |
Convert XML dump into a fairly normalized relational database
|
2024-12-12 |
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ucsc-pslfilter
|
public |
filter out psl file
|
2024-12-12 |
|
salmon
|
public |
Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
|
2024-12-12 |
|
ucsc-fatotwobit
|
public |
Convert DNA from fasta to 2bit format.
|
2024-12-12 |
|
ucsc-pslreps
|
public |
Analyze repeats and generate genome-wide best alignments from a
|
2024-12-12 |
|
svmlight
|
public |
SVMLight Library by Thorsten Joachim
|
2024-12-12 |
|
ucsc-parahubstop
|
public |
version 12.18
|
2024-12-12 |
|
r-qorts
|
public |
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq
datasets.
|
2024-12-12 |
|
iqtree
|
public |
Efficient phylogenomic software by maximum likelihood.
|
2024-12-12 |
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ucsc-genepredtogtf
|
public |
Convert genePred table or file to gtf.
|
2024-12-12 |
|
ucsc-taillines
|
public |
add tail to each line of file
|
2024-12-12 |
|
ucsc-mafsplitpos
|
public |
Pick positions to split multiple alignment input files
|
2024-12-12 |
|
r-rrbgen
|
public |
A lightweight limited functionality R bgen read/write library
|
2024-12-12 |
|
ucsc-netchainsubset
|
public |
Create chain file with subset of chains that appear in the net
|
2024-12-12 |
|
kmergenie
|
public |
KmerGenie estimates the best k-mer length for genome de novo assembly
|
2024-12-12 |
|
ucsc-bedremoveoverlap
|
public |
Remove overlapping records from a (sorted) bed file. Gets rid of
|
2024-12-12 |
|
fastahack
|
public |
No Summary
|
2024-12-12 |
|
pear
|
public |
paired-end read merger
|
2024-12-12 |
|
ucsc-pslstats
|
public |
collect statistics from a psl file.
|
2024-12-12 |
|
ucsc-netfilter
|
public |
Filter out parts of net. What passes
|
2024-12-12 |
|
tssar
|
public |
No Summary
|
2024-12-12 |
|
skesa
|
public |
Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment
|
2024-12-12 |
|
perl-xml-libxslt
|
public |
Interface to GNOME libxslt library
|
2024-12-12 |
|
ucsc-nettobed
|
public |
Convert target coverage of net to a bed file.
|
2024-12-12 |
|
tn93
|
public |
This is a simple program meant to compute pairwise distances between aligned nucleotide sequences in sequential FASTA format using the Tamura Nei 93 distance.
|
2024-12-12 |
|
sambamba
|
public |
Tools for working with SAM/BAM data
|
2024-12-12 |
|
migraine
|
public |
Implements coalescent algorithms for maximum likelihood analysis of population genetic data. The data currently handled are allelic counts but sequences will be handled in the forthcoming version.
|
2024-12-12 |
|
bowtie2
|
public |
A fast and sensitive gapped read aligner.
|
2024-12-12 |
|
libbambamc
|
public |
No Summary
|
2024-12-12 |
|
rnasnp
|
public |
No Summary
|
2024-12-12 |
|
novoalign
|
public |
Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms
|
2024-12-12 |
