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lambda
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public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
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2025-04-22 |
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dropletutils-scripts
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public |
CLI scripts for the DropletUtils package
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2025-04-22 |
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snp-pileup
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public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
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2025-04-22 |
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perl-math-utils
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public |
Useful mathematical functions not in Perl
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2025-04-22 |
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pysvmlight
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public |
Interface to Thorsten Joachims' SVM-Light
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2025-04-22 |
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unitas
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public |
unitas is a convenient tool for efficient annotation of small non-coding RNA sequence datasets produced by Next Generation Sequencing.
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2025-04-22 |
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kalign2
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public |
Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
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2025-04-22 |
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cat
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public |
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
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2025-04-22 |
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tmalign
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public |
TM-align sequence-order independent protein structure alignment.
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2025-04-22 |
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hiddendomains
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public |
hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains.
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2025-04-22 |
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sparcc
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public |
SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).
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2025-04-22 |
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cromwell-tools
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public |
Utilities for interacting with the Cromwell workflow engine
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2025-04-22 |
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r-cate
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public |
Provides several methods for factor analysis in high dimension (both n,p >> 1) and methods to adjust for possible confounders in multiple hypothesis testing.
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2025-04-22 |
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snver
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public |
SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data.
It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
Loci with any (low) coverage can be tested and depth of coverage will be quantitatively factored into final significance calculation.
SNVer runs very fast, making it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data.
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2025-04-22 |
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counterr
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public |
Counterr is a light-weight command line tool that computes errors in sequencing data by comparing the reads to a reference genome.
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2025-04-22 |
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var-agg
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public |
A simple helper for aggregating multi-sample VCF files into "site VCF" files.
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2025-04-22 |
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rvtests
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public |
Rare variant test software for next generation sequencing data
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2025-04-22 |
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r-epic
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public |
Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
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2025-04-22 |
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clinvar-tsv
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public |
A Snakemake-based program to download ClinVar and convert to easy-to-use TSV files.
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2025-04-22 |
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svim
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public |
SVIM is a structural variant caller for long reads.
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2025-04-22 |
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bioconductor-dropletutils
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public |
Utilities for Handling Single-Cell Droplet Data
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2025-04-22 |
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pyaavf
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public |
An amino acid variant format parser for Python.
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2025-04-22 |
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r-leapp
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public |
These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). "leapp" is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved.
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2025-04-22 |
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metaquantome
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public |
Quantitative metaproteomics analysis of taxonomy and function.
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2025-04-22 |
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r-mcpcounter
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public |
Estimating tissue-infiltrating immune and other stromal subpopulations abundances using gene expression
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2025-04-22 |
