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Current version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.

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The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. Functions can perform group comparison or individual sample analysis and visualization by fingerprint grid plot or fingerprint heatmap. Module repertoire analyses typically involve determining the percentage of the constitutive genes for each module that are significantly increased or decreased. As we describe in details;https://www.biorxiv.org/content/10.11

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This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

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Estimates differential gene expression for short read sequence count using methods appropriate for count data. If you have paired data you may also want to consider Tophat/Cufflinks. Input must be raw count data for each sequence arranged i

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MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features' levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry,

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The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully parsed lipid name and supplements it with LIPID MAPS Category and Class information. Also, the structural level and further structural details about the head group, fatty acyls and functional groups are returned, where applicable.

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Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metada

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the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.

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This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me

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cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat

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Provides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements

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Expert knowledge for Azure Internet Peering development including troubleshooting. Use when validating Peering Service prefixes, checking prefix registration, verifying routing, or fixing reachability issues, and other Azure Internet Peering related development tasks. Not for Azure ExpressRoute (use azure-expressroute), Azure Virtual Network (use azure-virtual-network), Azure Virtual WAN (use azure-virtual-wan), Azure VPN Gateway (use azure-vpn-gateway).

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Expert knowledge for Azure Education Hub development including troubleshooting, and limits & quotas. Use when managing Azure for Students credits, yearly quotas, renewals, or Dev Tools for Teaching sign-in issues, and other Azure Education Hub related development tasks. Not for Azure Lab Services (use azure-lab-services), Azure DevTest Labs (use azure-devtest-labs), Azure Virtual Desktop (use azure-virtual-desktop).

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Expert knowledge for Azure ExpressRoute development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring ExpressRoute circuits/gateways, BGP routing (incl. IPv6), FastPath, Global Reach, or MACsec/IPsec, and other Azure ExpressRoute related development tasks. Not for Azure Virtual Network (use azure-virtual-network), Azure Virtual WAN (use azure-virtual-wan), Azure VPN Gateway (use azure-vpn-gateway), Azure Internet Peering (use azure-internet-peering).

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Daily on-page and technical SEO audit of every page on a site - discovers URLs from the sitemap, scores each page, adds cross-page checks (duplicate titles, canonicals, sitemap gaps), diffs against yesterday, and sends the score line plus any regressions

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Compose and send a one-off email to a named recipient via Resend - written in the operator's voice, then sent in-run through the shared send caps with an operator audit copy

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Autonomous cloud-cost analyst across Neon, Vercel, Railway and GitHub Actions - pulls per-object usage, attributes it to the biggest drivers, root-causes each, and emits recommendations ranked by real signal (idle %, over-allowance, failure rate) with dollar figures only where the billing API returns real ones (and, armed, applies safe cost levers).

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Watch a list of competitor web pages on a cadence - snapshots each page's real signals (pricing, headings, CTAs, new/removed pages, title/description), diffs against the last run, and reports only what actually changed.

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Autonomous compute-reselling agent on Surplus Intelligence - resells free or low-cost provider compute across Bankr, AWS Bedrock, and Google Vertex (GCP) as one skill. Reads the live market + your cost + your usage, auto-lists your models per enabled provider, and reactively prices each offer to win routing within a cost floor, cap, and health guardrails.

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Reach into past AI conversation history through the `trellis mem` CLI. Use whenever the user asks 'how did we solve X last time', 'have we discussed this before', 'what was the decision on X', 'remind me what we did in this task', '上次怎么解的', '之前讨论过吗', '想起一段对话', or when starting a brainstorm that overlaps prior work, debugging a familiar bug, continuing a task across sessions, or doing a finish-work review. Returns raw past dialogue; decide for the moment whether to update spec, append to task notes, quote inline in the answer, or just internalize.

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Build prospect lists where the prospect is already one hop from the client, and write the line that says so. Seven members, each with its own source. Current-customer alumni is the priority member - everyone who ever worked at one of the client's customers or case-study companies and has since moved on. Triggers on "warm intro", "who do we know at that account", "they used to work at our customer", "alumni of our case study company", "shared investor angle", "who is in the same city as our rep", "did they visit our site". Outputs warm_intro_line plus a per-member evidence column.

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Always-on spam and deliverability guardrails for cold email copy. Apply these rules whenever writing, reviewing, or QA-ing subject lines, openers, follow-ups, CTAs, or any cold outreach copy. Trigger on phrases like "check this for spam", "spam word check", "deliverability review", "QA this copy", "flag banned words", "check subject line", "is this safe to send", "scan for spam triggers", or any time cold email copy is being generated or reviewed. Also trigger automatically as a background rule whenever the campaign-copywriting or cold-email-copywriting skill is active -- these guardrails apply to EVERY piece of outbound copy generated, even if the user does not explicitly ask for a check.

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Pulls replies from a Smartlead campaign, classifies each as positive/neutral/negative/OOO/bounce/unsubscribe using Claude, and reports the positive reply rate — the north-star metric for cold email. Use when the user wants to know if a campaign is actually working (not just getting replies, but getting the RIGHT replies). Triggers on "score my replies", "how's campaign X doing", "positive reply rate", "is this campaign working".

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Creates cold email copy through a stepwise confirmation process. Use when writing email campaigns, given a campaign strategy document, website, or client context. Confirms direction at each step before outputting final copy.

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