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scsnv-seq

scSNV-seq

segalign

A Scalable GPU System for Pairwise Whole Genome Alignments

segment-everything-everywhere-all-at-once

[NeurIPS 2023] Official implementation of the paper "Segment Everything Everywhere All at Once"

semantic-sam

[ECCV 2024] Official implementation of the paper "Semantic-SAM: Segment and Recognize Anything at Any Granularity"

seq2fun

an ultra-fast, all-in-one high resolution functional profiling tool directly from RNA-seq raw reads for organisms without reference genomes

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

seqtk

Toolkit for processing sequences in FASTA/Q formats

sequoia

Repository for the Sequoia phylogeny reconstruction pipeline

sequoia_notr

This Fortran program is the stand alone equivalent to the R package 'sequoia', and performs pedigree reconstruction from SNP data

seqyclean

To pre-process NGS data in order to prepare for downstream analysis.

shap

A game theoretic approach to explain the output of any machine learning model.

shasta

De novo assembly from Oxford Nanopore reads.

shinycircos

an R/shiny application for creation of Circos plot interactively

shinysyn

A shiny application to visualize MCscan result

singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.

siphynetwork

A birth-death-hybridization based phylogenetic network simulator.

smartie-sv

calling SVs from Blasr contig level alignments

snap

SNAP：Gene prediction software

snpr

population genomics basic stats

spedestem

Molecular species delimitation approaches

splash

split_genes

Split-gene misannotation pipeline

sqlitebrowser

Official home of the DB Browser for SQLite (DB4S) project. Previously known as "SQLite Database Browser" and "Database Browser for SQLite". Website at:

srf

SRF: Satellite Repeat Finder

srna-heterosis

This project contains all scripts and Java programs used for bioinformatics analyses in the publication: Seifert et al. (2018) Parental expression variation of small RNAs is negatively correlated with grain yield heterosis in a maize breeding population. Frontiers in Plant Science, doi: 10.3389/fpls.2018.00013

stainedglass

Make colorful identity heatmaps of genomic sequence

stanford_alpaca

Code and documentation to train Stanford's Alpaca models, and generate the data.

stringdecomposer

Tool for decomposition centromeric assemblies and long reads into monomers

subphaser

Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers.

sunflower_heterosis_2018

sunflower_heterosis