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[FEATURE]: Standalone vector store

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#3 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 1, 2025

[FEATURE]: Add Agent Memory and Workflow Context Management

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#31 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 5, 2025

[FEATURE]: Add Chunker

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Task

#32 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 5, 2025

[FEATURE]: Integrate Agent Framework Types into DeepAgent System

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#68 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[BIOINFO]: Vendor Bioinformatics Tools from BioContainers using BioinfoMCP Converter

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Improvement

Status: Open.

Feature

#130 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[FEATURE]: Implement DeepAgent System with Pydantic AI

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#60 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement DeepAgent Tools with Pydantic AI Integration

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Improvement

Status: Open.

Feature

#62 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement DeepAgent Prompts System with Template Management

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Improvement

Status: Open.

Task

#63 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement DeepAgent Specialized Agent Implementations

enhancementNew feature or requestNew feature or request

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#64 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Hydra Configuration for DeepAgent System

enhancementNew feature or requestNew feature or request

Feature

Improvement

Status: Open.

Feature

#65 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Bash Scripts for DeepAgent Deployment and Automation

enhancementNew feature or requestNew feature or request

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#66 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Comprehensive Integration Tests for DeepAgent System

help wantedExtra attention is neededExtra attention is needed

Improvement

Status: Open.

Task

#67 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Agent Framework Content Types Integration

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Task

#70 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Agent Framework Agent Run Response Types Integration

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Task

#71 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Agent Framework Chat Options Integration

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Task

#72 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[FEATURE]: Implement Agent Framework Usage Tracking Integration

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Task

#73 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 7, 2025

[BIOINFO]: Vendor bamCoverage from deepTools BioContainer

Status: Open.

#131 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor faToTwoBit from UCSC Genome Browser Tools

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#132 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor GATK ApplyBQSR from Genome Analysis Toolkit

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#133 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor GATK BaseRecalibrator from Genome Analysis Toolkit

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#134 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor GATK SelectVariants from Genome Analysis Toolkit

enhancementNew feature or requestNew feature or request

Feature

good first issueGood for newcomersGood for newcomers

Status: Open.

Feature

#136 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor MultiQC quality control report aggregation tool

enhancementNew feature or requestNew feature or request

Feature

good first issueGood for newcomersGood for newcomers

Status: Open.

Feature

#139 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor plotCorrelation from deepTools

duplicateThis issue or pull request already existsThis issue or pull request already exists

enhancementNew feature or requestNew feature or request

Feature

Status: Open.

Feature

#140 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor QUAST genome assembly assessment tool

enhancementNew feature or requestNew feature or request

Feature

good first issueGood for newcomersGood for newcomers

Status: Open.

#141 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025

[BIOINFO]: Vendor Trimmomatic read trimming and filtering tool

Feature

good first issueGood for newcomersGood for newcomers

help wantedExtra attention is neededExtra attention is needed

Status: Open.

Feature

#142 In DeepCritical/DeepCritical;

· Josephrp opened on Oct 12, 2025