bio-machine-learning-atlas-mapping
Map query cells to reference atlases with scANVI or Symphony.
Maintainer K-Dense Inc. · Last updated April 1, 2026
This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libraries, and detailed examples, see REFERENCE.md. If you need to fill out a PDF form, read FORMS.md and follow its instructions.
Original source
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pdf
Skill Snapshot
Source Doc
from pypdf import PdfReader, PdfWriter
## Extract text
text = ""
for page in reader.pages:
text += page.extract_text()
import pandas as pd
with pdfplumber.open("document.pdf") as pdf:
all_tables = []
for page in pdf.pages:
tables = page.extract_tables()
for table in tables:
if table: # Check if table is not empty
df = pd.DataFrame(table[1:], columns=table[0])
all_tables.append(df)
Related skills
Map query cells to reference atlases with scANVI or Symphony.
Align short reads to reference genome with BWA-MEM.
Download, index, and manage reference genome FASTA files.
This skill provides efficient Python-based tools for searching and retrieving preprints from the bioRxiv database. It enables comprehensive…