T

C library and command line tools for high-throughput sequencing data formats.

an interactive tool for the identification of meaningful parameters in topologically-associating domains (TADs) algorithms for Hi-C data

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

TargetP-2.0 server predicts the presence of N-terminal presequences: signal peptide (SP), mitochondrial transit peptide (mTP), chloroplast transit peptide (cTP) or thylakoid luminal transit peptide (luTP). For the sequences predicted to contain an N-terminal presequence a potential cleavage site is also predicted.

TEcandidates is a pipeline to include transposable elements in RNA-seq differential expression analysis.

Python is an interpreted, high-level, general-purpose programming language. This environment includes most common libraries for data manipulations (Pandas, Numpy), data visualization (Matplotlib, Seaborn, Altair, Plotly and Bokeh) and machine learning (Tensorflow, PyTorch, Scikit).

TensorFlow is an end-to-end open source platform for machine learning.

Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg

compute RNA read count for transposable elements and Differential expression analysis of transposable elements

An easy way to get up and running with the TeX document production system

A dynamic programming language with GUI support. Bundles Tcl and Tk.

A terminal multiplexer.

A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python

A pipeline for particle detection in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Topaz also includes methods for micrograph denoising using deep denoising models.

A spliced read mapper for RNA-Seq

A post sequencing QC tool for Oxford Nanopore sequencers

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

Reference free quality assessment of de-novo transcriptome assemblies

TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.

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Transposable Elements MOvement detection using LOng reads

Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control

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A flexible read trimming tool for Illumina NGS data

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms

TCR and BCR assembly from bulk or single-cell RNA-seq data

Structural variant comparison tool for VCFs

Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes

Infer tree sequences

The tree sequence toolkit.

reports the length of each scaffold and the gap locations stored in a twoBit Sequence Archive

Convert all or part of .2bit file to fasta