SpecialtyDox Help Center

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First Login

After signup, log in with your admin credentials. You'll land on the main dashboard. From here you can:

• Add providers and staff under Settings > Users
• Configure your practice info (NPI, Tax ID, address) under Settings > Practice
• Start adding patients immediately

SpecialtyDox is a complete clinical platform with seven integrated products:

All products share the same patient chart, user accounts, and database. No data silos.

Complete These Steps on Day One

After login, you land on the main dashboard. The dashboard provides an at-a-glance view of your practice:

• Today's appointments with status (scheduled, confirmed, checked-in, completed)
• Clinical inbox showing urgent tasks and unread items
• RTM alerts for patients needing attention
• Recent encounters that need review or signing

Use the top navigation bar to access different modules. The sidebar (if visible) provides quick links to common actions.

For HIPAA compliance, your session automatically expires after 15 minutes of inactivity. When this happens, you'll be redirected to the login page.

• Sessions are secured with encrypted tokens
• Login attempts are rate-limited (10 attempts per 15 minutes)
• All logins are recorded in the audit log

Open a patient's chart and click Edit or select the field you want to update. You can modify:

• Demographics (name, DOB, address, phone, email)
• Insurance (primary and secondary plans, member IDs, group numbers)
• Clinical info (diagnosis, allergies, medications, pharmacy)
• Emergency contacts
• Provider assignment
• Patient status (active/inactive)

All changes are logged in the audit trail.

Patients can access a limited portal using their last name and date of birth. Through the portal, patients can:

• View upcoming appointments
• View test results and documents
• Send and receive messages
• Update their own phone, email, address, and emergency contacts
• View medical information (read-only)

Patients cannot modify clinical data, diagnoses, or insurance information through the portal.

Uploading Documents

Navigate to the patient chart and open the Documents tab. Click Upload to add files.

Supported categories include:

• Reports, Lab Results, Imaging
• Forms, Prior Authorization
• Correspondence, Referral Letters
• Insurance Cards, Consent Forms

Document Workflow

Documents can be reviewed and signed by providers. Track review status, add tags, and associate documents with specific encounters.

Documents are stored encrypted in AWS S3 with role-based access controls.

Each appointment progresses through workflow stages:

Each stage is timestamped for reporting and workflow tracking.

The system can send automated SMS appointment reminders. Reminders include the date, time, and visit type. Patients can reply to:

• Confirm their appointment
• Reschedule (a staff member follows up)
• Opt out of future reminders

Configure reminder timing (e.g., 2 days before) in your practice settings.

Encounters are clinical documentation records for patient visits. To create one:

• Chief Complaint — Why the patient is being seen
• History of Present Illness (HPI) — Clinical narrative
• Vitals — BP, HR, Temp, RR, O2 sat, weight, BMI
• Review of Systems (ROS) — By organ system
• Physical Exam — Findings by system
• Assessment & Plan — Diagnoses and next steps
• Prescriptions — New or changed medications
• CPT & ICD-10 Codes — For billing

Signing an Encounter

Click Sign & Finalize to electronically sign the encounter. This records the provider name, date, and time. Once signed, the encounter is locked from editing.

Addenda

Need to add information to a signed encounter? Click Add Addendum. Addenda are timestamped additions that don't modify the original note — they append corrections or additional information.

For sleep medicine encounters, you can include CPAP/BiPAP device data:

• Usage hours, AHI, leak rate, pressure settings
• Compliance percentage (days with 4+ hours usage)
• Sleep diary data (bedtime, wake time, quality rating)

This data can be pulled from RTM records or entered manually.

Three Ways to Capture the Encounter

• Live Recording — Click the microphone button to record in real time. The system provides live transcription as you speak.
• Upload Audio — Upload a WebM audio file from another recording device. AWS Transcribe processes it automatically.
• Paste Transcript — Paste or upload a text transcript (.txt, .doc, .docx) directly.

After recording or uploading a transcript:

• Chief Complaint / HPI
• Subjective Report
• Vitals
• Medications / Medication Reconciliation
• Review of Systems
• Physical Exam / Mental Status Exam
• Screening Scores (PHQ-9, GAD-7, ISI, ESS, STOP-BANG, etc.)
• Assessment with ICD-10 codes
• Plan with numbered action items

When the note is ready:

Templates control the structure and AI behavior for note generation.

Creating a Template

1. Go to Settings > Templates
2. Click + New Template or Clone an existing global template
3. Set the specialty, template type (SOAP, HPI Only, Procedure Note, etc.), and clinical focus
4. Define sections (each has a name, AI prompt, and field type: narrative or list)
5. Configure the macro library for quick-insert phrases
6. Select scoring tools to recognize (PHQ-9, GAD-7, ISI, etc.)
7. Click Auto-Generate System Prompt to create specialty-appropriate AI instructions, or write your own
8. Save the template

After generating a note, you can create a patient-friendly summary letter:

• Click Patient Letter to auto-generate a plain-language summary
• The letter includes: visit summary, key findings, instructions, medication changes, and follow-up recommendations
• Actions: Copy to clipboard, Print, or Download
• Formatted in a professional letter style suitable for handing to the patient

Clinical Inbox

The inbox shows clinical tasks and alerts assigned to you or your team. Create tasks with a subject, body, priority (urgent/high/normal), and due date. Assign to specific users or leave in the general pool.

Work Buckets

Work is organized into category queues:

• Faxes — Inbound/outbound fax routing and processing
• Prescription Refills — Refill requests from patients/pharmacies
• Messages — Patient messages requiring response
• Records Requests — Medical records requests
• Other — Custom tasks

Each item has a priority level (stat, urgent, high, normal) and due date. The dashboard shows team workload statistics: total open, urgent count, new today, and overdue items.

How Check-Ins Work

The system sends a daily SMS personalized by diagnosis:

• PAP patients: Sleep rating → CPAP hours → Mask issues → Energy level
• CBT-I patients: Sleep rating → Sleep onset time → Awakenings → Energy level

After the patient responds, the AI coaching engine generates a personalized clinical response. Safety flags (crisis, PHQ-2 positive, escalation) trigger immediate provider alerts.

RTM data days are critical for billing. Each day a patient reports data counts as one data day. You can also manually enter device data:

• Usage hours — How long the device was used
• AHI — Apnea-Hypopnea Index (events/hour)
• Leak rate — L/min
• Pressure — Average and 95th percentile

A day with 4+ hours usage is marked as compliant. The system auto-calculates monthly compliance percentage.

RTM CPT Codes

Auto-Generating RTM Claims

The RTM Roster shows all enrolled patients with current-month metrics:

• Data days count (toward 16-day threshold)
• Average usage hours
• Average AHI
• Compliance percentage
• Message count

Filter by program type to view subsets. The RTM Summary Report identifies which patients are billable this month and shows claims status.

Track clinical time spent on RTM patients to support billing:

• Go to the patient's RTM record and click + Activity
• Select activity type: coaching, troubleshooting, review, etc.
• Enter a description and duration in minutes
• Save the activity

Total monthly minutes determine eligibility for 98980 (20+ min) and 98981 (40+ min) codes.

Billable Codes

Log each care management activity with:

• Activity type (outreach, assessment, monitoring, care coordination)
• Staff member who performed the activity
• Duration in minutes
• Description of what was done

The system auto-calculates total monthly minutes and determines which CPT code applies. View the monthly billing summary to see billable status for each enrolled patient.

Therapy Sessions

For each session, record: session and week number, protocol focus area, ISI and sleep efficiency scores, session notes, homework assigned, techniques introduced, and patient adherence level. Scores auto-update the patient's progress record.

Sleep Diary

Patients log daily sleep data including bedtime, lights-out time, sleep onset latency, awakenings, wake-after-sleep-onset (WASO), final wake time, total sleep time, sleep quality rating, and lifestyle factors (caffeine, alcohol, exercise). Sleep efficiency is auto-calculated. View up to 60 days of diary history per patient.

AI Recommendations

Request AI-generated clinical recommendations based on the patient's data. The AI reviews progress, suggests protocol adjustments, behavioral interventions, and includes risk assessments (including OSA screening via STOP-BANG).

DoxBilling has 12 tabs for managing all billing operations:

Key Metrics

• Patient Revenue (YTD) — Total billed with claim count
• Claims Paid — Count and dollar amount collected
• Claims Pending — Awaiting payer response
• Denied / At Risk — Claims needing attention

Revenue by Category

Revenue is automatically broken down by CPT code category: RTM, Psychotherapy, Screenings, DMHT, and E/M.

Billing Insights

Auto-generated alerts appear based on patient data:

• Green: "Patient has 22 RTM days — exceeds 16-day threshold. Eligible for 99457+99458."
• Orange: "Patient has 12 RTM days — needs 4 more to reach billable threshold."
• Red: "3 denied claims. $1,200 at risk. Review denials tab."

Option A: Auto-Generate RTM Claims

Option B: Create from Auto-Coder

Option C: Manual Claim Entry

Submitting

Click Submit 837 on any draft claim. The system generates an X12 837P EDI file with all required segments (ISA, GS, ST, BHT, patient demographics, diagnosis codes, and line items). The claim status changes to "Submitted."

Manual Payment Entry

Record payments with: claim ID, check number, paid amount, allowed amount, deductible, coinsurance, EOB date, and notes. The system auto-calculates patient balance.

ERA/835 Auto-Posting

For electronic remittance files from payers:

The Auto-Coder analyzes your encounter documentation and recommends CPT codes based on CMS billing rules.

Coding Logic

RTM Visits (16+ data days):

• 40+ min documented → 99457 ($50.94) + 99458 ($41.76)
• 20-39 min documented → 99457 only
• Always includes 98978 ($55.72) for respiratory device supply
• Below 16 days → codes are blocked with explanation

Mental Health:

• 53+ min → 90837 ($148.20)
• 38-52 min → 90834 ($110.40)
• Screening tools (PHQ-9, GAD-7, ISI, DBAS) → 96127 ($5.44 each, up to 4 units)

Real-time eligibility checking is available via the Stedi healthcare EDI integration:

Results Include

• Plan information and active/inactive status
• Deductible: individual and family, met and remaining amounts
• Out-of-pocket maximums
• Copays by visit type
• Coinsurance percentage
• Prior authorization requirements

Viewing Denials

The Denials tab shows all denied claims with: denial reason, denial code, claim ID, payer, status, appeal deadline, and billed amount.

Common Denial Codes

Filing an Appeal

Dashboard KPIs

• Active Devices — Total assigned devices
• Active Patients — Patients with data in last 7 days
• 30-Day Compliance Rate — Medicare compliance percentage
• Average Usage & AHI — Last 7 days
• Open Alerts — Critical and warning alerts
• Pending Orders — Orders in progress
• Resupply Due — Items eligible for reorder

Key Pages

• Population — All patients filtered by status (compliant, at-risk, lost to follow-up, new setup)
• Compliance — 90-day compliance calendars per patient
• Intake — Referral processing queue
• Orders & Supply — Orders, inventory, product catalog, deliveries, resupply
• Auth & Docs — Prior auth, CMN tracking, document vault
• Analytics — Compliance trends, usage distribution, AHI breakdown
• Tasks — Work queues by category

New referrals progress through stages:

Each intake tracks a document checklist (insurance verified, Rx on file, sleep study, face-to-face, CMN, delivery ticket).

Order Status Flow

Draft → Pending Auth → Authorized → Ordered → Shipped → Delivered (or Cancelled)

The system automatically tracks resupply eligibility based on Medicare intervals:

• Masks: every 90 days
• Cushions: every 30 days
• Headgear: every 180 days
• Tubing: every 90 days
• Filters: every 30 days (disposable) / 180 days (reusable)

When a patient's supplies become eligible, they appear in the Resupply queue. Staff can contact patients and create reorders with one click. After delivery, the next resupply date is auto-calculated.

Prior Authorization

Track prior auth requests with: payer, HCPCS codes, status (pending/submitted/approved/denied/appealed), auth number, decision date, effective/expiration dates, and approved quantities. The dashboard alerts you when auth is expiring within 30 days.

Certificate of Medical Necessity (CMN)

Medicare requires a signed CMN for CPAP equipment. Track: CMN type (initial/renewal/revised), diagnosis codes, ordering physician, effective/expiration dates, and physician signature status. The dashboard alerts when a CMN is expiring.

Manual Entry

Enter daily data per patient: date, usage hours, AHI, leak rate, and pressure readings.

Batch CSV Upload

Upload CSV exports from ResMed AirView or SD card data. Required columns: date, usage_hours, ahi, leak. Optional: leak_95, pmin, pmed, p95, pmax.

Color coding: green for nights with 4+ hours usage, red for under 4 hours.

Medicare requires patients to demonstrate CPAP compliance within the first 90 days: 4+ hours of usage on 21 of 30 consecutive days.

DoxDME provides a visual compliance calendar:

• Green — 4+ hours (compliant night)
• Red — Under 4 hours (non-compliant)
• Gray — No data uploaded
• White — Future dates

The system shows: days compliant/total, compliance percentage, days remaining in the 90-day period, and overall pass/fail status.

Alerts

Automatic alerts trigger when a patient is at risk of failing compliance, has missed consecutive nights, or has failed the compliance period.

The DoxFinance dashboard shows key financial metrics at a glance:

• Revenue — This month, last month, and YTD with trend percentage
• Expenses — This month and YTD
• Net Income — This month and YTD
• A/R Outstanding — Unpaid invoices
• A/P Outstanding — Unpaid bills

Dashboard Widgets

• Revenue vs. Expenses chart
• Bank accounts with current balances
• Bills due soon (next 10 by due date)
• Recent journal entries (last 10)
• EHR Revenue Sync status

The Chart of Accounts (COA) is pre-seeded with healthcare-specific accounts. You can add, edit, or deactivate accounts.

Account Types

Each account has a number, name, type, sub-type, normal balance direction (debit/credit), and current balance calculated from journal entries.

Creating a Journal Entry

Reversing an Entry

Click Reverse on any posted entry. A new entry is created with opposite debit/credit amounts, and the original is marked as reversed.

Period Close

Close accounting periods to prevent retroactive changes. Admin users can reopen periods if needed.

Available Reports

All reports can be exported to CSV for your accountant or tax preparer.

Adding a Vendor

Go to Payables > Vendors and click + Add Vendor. Enter: name, type, contact info, Tax ID, payment terms (Net 30 default), default GL account, and whether they require a 1099.

Creating a Bill

Go to Payables > Bills. Select the vendor, enter bill number, amount, due date, and GL account. Bills track status: Pending → Partial → Paid.

Paying a Bill

Click Pay on a bill. Enter the amount, payment method (check/ACH/wire/card), reference number, and bank account. The system auto-creates a GL journal entry (debit AP, credit Cash) and updates the vendor's YTD payments.

Create invoices for patient balances or other receivables. Track invoice number, client name, amount, due date, and status (draft/sent/partial/paid/overdue). Record payments received with date, method, and amount. The system auto-updates invoice status and A/R totals.

DoxFinance can automatically sync revenue from DoxBilling into the general ledger:

Add bank accounts (checking/savings) with institution name, account/routing numbers, and current balance. Import bank transactions via CSV upload, then reconcile by marking transactions as matched. Track deposits and withdrawals with payee, category, and reconciled status.

• Hours: Regular, Overtime, PTO
• Gross Pay: Auto-calculated from hours x rate, or enter manually
• Taxes: Federal (default 22%), State (0% for Texas), Social Security (6.2%), Medicare (1.45%)
• Deductions: 401(k), insurance, garnishments, etc.
• Payment Method: Direct deposit, check, or cash

What Happens on Approval

• The period is locked from further changes
• A GL journal entry is auto-created: Salary Expense (debit), Payroll Taxes Payable (credit), Cash (credit)
• Account balances update immediately

Go to Payroll > Employees to manage your team.

Adding an Employee

Click + Add Employee and fill in:

• Name, email, phone
• Employee type: W-2 or 1099 Contractor
• Department and job title
• Pay type (salary/hourly), pay rate, and frequency (weekly/biweekly/semimonthly/monthly)
• Hire date
• Link to a provider record (if they're also a clinical provider)

Track PTO balance, PTO accrual rate, and sick leave balance per employee.

The HR Dashboard provides a quick view of your workforce:

• Total Employees and Active Count
• Certifications Expiring within 90 days
• Pending Time Off Requests awaiting approval
• Recent Hires (last 90 days)

Each employee has a comprehensive profile with tabs:

• Personal Info: Name, DOB, gender, marital status, ethnicity, veteran/disability status
• Job Info: Title, department, pay info, hire date, supervisor, location
• Contact: Address, phone, email
• Emergency Contacts: Name, relationship, phone, primary flag
• Documents: I-9, W-4, offer letters, NDAs, signed policies (with e-signature tracking)
• Certifications: Licenses, credentials, CE tracking, expiration alerts
• Time Off: PTO requests, balances, accrual history
• Benefits: Health, dental, vision, 401(k), HSA enrollments
• Onboarding: Checklist of required tasks
• Performance Reviews: Annual/mid-year reviews with ratings and goals
• Incidents: Disciplinary records and documentation

When a new employee is added, click Seed Onboarding Checklist to auto-populate healthcare-specific onboarding tasks:

• I-9 Verification
• Background Check
• Drug Screening
• Equipment & Access Provisioning
• Benefits Enrollment
• NDA & IP Agreements
• Credentials Verification
• HIPAA Training
• EMR Training
• Office Tour
• Handbook Acknowledgment

Mark each item complete as the employee progresses. Upload signed documents directly to their profile.

Submitting a Request

Go to the employee's profile > Time Off tab. Enter start/end dates, hours, type (Vacation, Sick, Personal, Bereavement, Unpaid), and reason.

Approving Requests

Managers see pending requests on the HR Dashboard. Click to review, then Approve or Reject. Approved time is tracked against the employee's PTO balance.

Track employee certifications, licenses, and continuing education:

• Add certification type (License, Certification, CE), name, issuing body, credential number
• Set issue and expiration dates
• Track CE requirements: hours required vs. hours completed
• Set reminder days (alerts before expiration)
• Upload a copy of the credential

The Expiring Certifications widget on the HR Dashboard shows all credentials expiring within 90 days, giving you time to coordinate renewals.

Create performance reviews with: review date, period (annual, mid-year, 90-day), reviewer, overall rating, comments, goals, and development areas. Reviews can be saved as drafts or marked completed.

The Compliance Dashboard gives you a real-time view of your practice's regulatory status:

• Upcoming Deadlines — Next 30 days from the compliance calendar
• HIPAA — Expired training count, BAAs needing review, open breaches
• OSHA — Open incident count
• FMLA — Active leave cases
• COBRA — Open qualifying events
• Garnishments — Active wage garnishments
• New Hire Reports — Pending filings
• Handbook Acknowledgments — Percentage of employees who have signed

The compliance calendar tracks all regulatory deadlines. Click Seed Calendar on first use to auto-populate 25+ healthcare-specific deadlines:

• Tax: W-2/1099 filing, quarterly 941s, estimated taxes, franchise tax, FUTA
• OSHA: 300A posting (Feb 1-Apr 30), 300 log review, bloodborne pathogens training
• HIPAA: Annual risk assessment, security training
• Benefits: Open enrollment, ACA 1095-C
• Insurance: Workers comp and malpractice renewals
• Credentials: DEA registration and CLIA renewal checks
• Labor: Poster updates, I-9 re-verification

Add custom deadlines with title, category, due date, recurrence, responsible person, and reminder days. Mark items complete as you finish them.

Training Records

Track HIPAA training for all staff: training type (Privacy, Security, Breach Notification), completion date, expiration date, score/pass-fail, and certificate URL. The dashboard alerts you when training is expired.

Business Associate Agreements (BAAs)

Every vendor with access to PHI must have a signed BAA. Track: vendor name, service description, effective/termination dates, review date, and signed BAA file. Status: active, pending signature, expired, or terminated.

Breach Log

Document any PHI breach with: incident and discovery dates, description, individuals affected, type (accidental disclosure, theft, hacking), corrective action, HHS reporting status, and notification dates. Track through investigation to resolution.

Record workplace injuries and illnesses for OSHA compliance:

• Employee, incident date, injury type, body part affected, location
• Description, treatment provided
• Days away from work, days of restricted work
• OSHA recordable determination (Form 300 log)

This maintains your OSHA 300 log required for annual posting (February 1 through April 30).

FMLA

Track employee leave: type (medical, family care, military, parental), start/end dates, intermittent flag, total hours used, certification received, recertification due date, and status.

Workers Compensation

File and track claims: injury details, claim number, carrier, policy number, physician, treatment, status (filed/approved/denied/settled/closed), and amounts.

COBRA

Record qualifying events: type (termination, reduction in hours, etc.), election deadline (60 days), monthly premium, benefits continued, and election status.

Wage Garnishments

Track court-ordered deductions: type (child support, tax levy, student loan), case number, amounts (fixed or percentage), priority order, and remaining balance.

New Hire Reporting

File new hire reports with the state (Texas: within 20 days of hire). Track: employee, state, hire date, report date, and confirmation number.

Employee Handbook

Upload handbook versions, track which version is current, and require employee acknowledgment with e-signature. The compliance dashboard shows the percentage of employees who have signed.

Labor Law Postings

Track required postings (federal and state). Click Seed Postings to auto-populate required notices: minimum wage, EEOC, FMLA, ADA, OSHA, WARN Act, and Texas-specific postings.

Creating a User

Password Requirements

Passwords must be 8+ characters with at least one uppercase letter, one lowercase letter, and one number.

Deactivating Users

Deactivate (don't delete) users who leave. This preserves audit history while preventing further login.

Changing Your Own Password

Go to Settings > Security. Enter your current password, then your new password (twice). Click Change Password.

Resetting Another User's Password (Admin)

Go to Settings > Users, select the user, and click Reset Password. Enter a temporary password. The user should change it on their next login.

The audit log records all significant system actions for HIPAA compliance. View the last 200 entries under Settings > Audit Log.

Each entry includes: timestamp, user, action type, details, and IP address.

Tracked actions include: login/logout, patient creation/deletion, user management, data changes, and document access.

Adding a Provider

Go to Providers and click + Add Provider. Enter:

• Name and credentials (MD, DO, NP, PA, etc.)
• NPI (National Provider Identifier) and Tax ID
• License: number, state, expiration date
• DEA: number and expiration date
• Specialty and department
• Contact info (email, phone)

Provider Credentials

Track additional credentials (board certifications, CAQH, etc.) with issuing body, credential number, issue/expiry dates, and status.

Payer Enrollments

Track each provider's enrollment with insurance payers: payer name, enrollment status (pending/active/recredentialing), application and effective dates, CAQH ID, and recredential dates.

Manage your payer relationships under Payers:

• Contracts: Track contract type (in-network/out-of-network), effective dates, auto-renewal, and contact info
• Fee Schedules: Store allowed amounts by CPT code for each payer, Medicare rates, and percentage of Medicare

Fee schedules are used by the billing module to calculate expected reimbursement.

Go to Settings > Practice to configure:

• Practice name, NPI, Tax ID
• Address, phone, email, website
• Departments list
• Features enabled

In DoxFinance, go to Settings > Company (admin only) to configure:

Business Information

Legal name, DBA, entity type (LLC, PLLC, S-Corp, C-Corp, etc.), state of incorporation, date established.

Tax & Federal IDs

EIN, State Tax ID, NPI, Taxonomy Code, Medicare/Medicaid Provider IDs, CLIA Number, IRS Filing Type.

Owner/Responsible Party

Owner name, title, SSN last 4 (for W-9), contact info.

Banking & Accounting

Bank name, routing/account numbers, fiscal year start month, accounting method (cash/accrual/hybrid), payroll frequency.

View which products are enabled for your practice. Each product (RTM, CCM, CBT-I, Scribe, Billing, Finance, HR, DME) has a subscription with:

• Tier: Trial, Starter, Professional, Enterprise
• Status: Active or Inactive
• Seats: Number of concurrent users allowed
• Patient Limit: Maximum patients (if applicable)

Contact support to upgrade your plan or add products.