NEEDLE-ESTIMATE(1)

🌸 NAME 🌸

okay bestie, so this is needle-estimate — a super cute little tool from the needle-estimate manual page that estimates the expression value of a transcript based on the Needle index. that's the whole vibe. no cap.

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📍 POSITIONAL ARGUMENTS

• ARGUMENT-1 (std::filesystem::path) — bestie. please. hand over a sequence file. that's the one thing she needs from you, don't leave her hanging 🥺

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✨ OPTIONS ✨

💖 Basic options:

• -h, --help — prints the help page. the classic. your bestie when you're lost 🫶
• -hh, --advanced-help — prints the help page including the advanced options. the deluxe version, the director's cut 👑
• --version — prints the version information. so you know exactly which era of this tool you're living in ⭐
• --copyright — prints the copyright/license information. legal girlies stay winning 💅
• --export-help (std::string) — exports the help page information. the value must be one of [html, man] — no other choices, she's picky 🙈
• -i, --in (std::filesystem::path) — the directory where input files can be found. Default: "./" 📂
• -o, --out (std::filesystem::path) — the directory where output files should be saved. Default: "expressions.out" 💾
• -t, --threads (unsigned 8 bit integer) — number of threads to use. Default: 1. Default: 1. (yes bestie, she really said it twice — Default: 1. it's giving redundancy, but we respect it 🔥)
• -m, --normalization-mode — set this if normalization is wanted. normalization is achieved bydividing the expression value with the expression threshold of the first ibf. it only makes sense if every bin has its own expression thresholds (which is the case if expression thresholds were generated automatically). Default: False. so like, don't just turn it on for fun, check that your bins are set up for it first 🎀

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🦋 VERSION

• Last update: 2024-11-07
• needle-estimate version: 1.0.3
• SeqAn version: 3.4.0

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🎀 URL

https://github.com/seqan/needle

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👑 LEGAL

• needle-estimate Copyright: BSD 3-Clause License
• Author: Mitra Darvish
• SeqAn Copyright: 2006-2025 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
• In your academic works please cite: Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments; Mitra Darvish, Enrico Seiler, Svenja Mehringer, René Rahn, and Knut Reinert; Bioinformatics, Volume 38, Issue 17, 1 September 2022, Pages 4100-4108. doi: https://doi.org/10.1093/bioinformatics/btac492

For full copyright and/or warranty information see --copyright. fr fr, go read it 💜

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okay that's the whole page bestie, no notes ✨ this was needle-estimate version 1.0.3, last updated 2024-11-07 (and it lives in the NEEDLE-ESTIMATE(1) manual, iykyk). go estimate some expressions, you absolute icon 🌈💖