diff --git a/_sources/api/rds2py.rst.txt b/_sources/api/rds2py.rst.txt
index 9fb0e0c..e468171 100644
--- a/_sources/api/rds2py.rst.txt
+++ b/_sources/api/rds2py.rst.txt
@@ -4,6 +4,14 @@ rds2py package
 Submodules
 ----------
 
+rds2py.granges module
+---------------------
+
+.. automodule:: rds2py.granges
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 rds2py.interface module
 -----------------------
 
diff --git a/api/modules.html b/api/modules.html
index 23679dd..fc00608 100644
--- a/api/modules.html
+++ b/api/modules.html
@@ -205,6 +205,7 @@ <h1>rds2py<a class="headerlink" href="#rds2py" title="Link to this heading">#</a
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="rds2py.html">rds2py package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="rds2py.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rds2py.html#rds2py-granges-module">rds2py.granges module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rds2py.html#rds2py-interface-module">rds2py.interface module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rds2py.html#rds2py-parser-module">rds2py.parser module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="rds2py.html#rds2py-pdf-module">rds2py.pdf module</a></li>
diff --git a/api/rds2py.html b/api/rds2py.html
index a106843..8a3174f 100644
--- a/api/rds2py.html
+++ b/api/rds2py.html
@@ -204,6 +204,9 @@ <h1>rds2py package<a class="headerlink" href="#rds2py-package" title="Link to th
 <section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading">#</a></h2>
 </section>
+<section id="rds2py-granges-module">
+<h2>rds2py.granges module<a class="headerlink" href="#rds2py-granges-module" title="Link to this heading">#</a></h2>
+</section>
 <section id="rds2py-interface-module">
 <h2>rds2py.interface module<a class="headerlink" href="#rds2py-interface-module" title="Link to this heading">#</a></h2>
 </section>
@@ -267,6 +270,7 @@ <h2>Module contents<a class="headerlink" href="#module-contents" title="Link to
             <ul>
 <li><a class="reference internal" href="#">rds2py package</a><ul>
 <li><a class="reference internal" href="#submodules">Submodules</a></li>
+<li><a class="reference internal" href="#rds2py-granges-module">rds2py.granges module</a></li>
 <li><a class="reference internal" href="#rds2py-interface-module">rds2py.interface module</a></li>
 <li><a class="reference internal" href="#rds2py-parser-module">rds2py.parser module</a></li>
 <li><a class="reference internal" href="#rds2py-pdf-module">rds2py.pdf module</a></li>
diff --git a/searchindex.js b/searchindex.js
index 3d1494b..520d927 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api/modules", "api/rds2py", "authors", "changelog", "contributing", "index", "license", "readme", "tutorial"], "filenames": ["api/modules.rst", "api/rds2py.rst", "authors.md", "changelog.md", "contributing.md", "index.md", "license.md", "readme.md", "tutorial.md"], "titles": ["rds2py", "rds2py package", "Contributors", "Changelog", "Contributing", "rds2py", "License", "rds2py", "Tutorial"], "terms": {"packag": [0, 3, 4, 5, 7, 8], "submodul": [0, 7], "interfac": [0, 4], "modul": [0, 4, 5], "parser": [0, 3], "pdf": 0, "content": [0, 4], "jkanch": 2, "jayaram": 2, "kancherla": 2, "gmail": 2, "com": [2, 4], "thi": [3, 4, 5, 6, 7, 8], "releas": 3, "migrat": 3, "more": [3, 4, 7, 8], "palat": 3, "googl": 3, "": [3, 4, 5, 7], "python": [3, 4, 5, 7], "style": [3, 4], "guid": [3, 4], "A": [3, 6], "major": [3, 4], "modif": 3, "i": [3, 4, 5, 6, 7, 8], "case": [3, 4], "all": [3, 4, 6], "camelcas": 3, "properti": [3, 7, 8], "method": [3, 4, 8], "function": [3, 4, 7, 8], "paramet": 3, "ar": [3, 4, 8], "now": [3, 7, 8], "snake_cas": 3, "In": [3, 4, 7], "addit": [3, 4, 7, 8], "docstr": [3, 4], "document": [3, 5, 6, 7], "ha": [3, 7], "been": [3, 4, 7], "updat": [3, 4], "us": [3, 4, 5, 6, 7, 8], "sphinx": [3, 4], "featur": [3, 4], "link": [3, 4], "object": [3, 5, 7, 8], "type": 3, "also": [3, 4, 8], "privat": [3, 4], "special": 3, "dunder": 3, "e": [3, 4], "g": [3, 4], "__getitem__": 3, "__copy__": 3, "etc": 3, "intersphinx": 3, "refer": [3, 4, 5], "from": [3, 4, 5, 6, 7, 8], "depend": [3, 4, 7], "configur": [3, 4], "flake8": [3, 4], "ruff": 3, "black": [3, 4], "ad": [3, 4], "pyproject": 3, "toml": 3, "setup": [3, 4, 7], "cfg": [3, 4], "less": 3, "annoi": 3, "final": 3, "pyscaffold": [3, 4, 7], "myst": [3, 4], "markdown": 3, "compil": [3, 4], "instead": [3, 4], "recommonmark": 3, "As": 3, "part": [3, 4], "one": [3, 4, 7, 8], "mai": [3, 4], "pre": [3, 4], "commit": [3, 4], "run": [3, 4, 7], "some": [3, 8], "routin": 3, "task": [3, 5], "lint": 3, "format": 3, "befor": [3, 4], "everi": 3, "while": [3, 4], "sometim": [3, 4], "can": [3, 4, 5, 7, 8], "ignor": 3, "verifi": 3, "bring": 3, "consist": 3, "code": [3, 5], "base": [3, 4, 7, 8], "fix": [3, 4], "nasti": 3, "bug": [3, 4], "1729": 3, "add": [3, 4, 8], "your": 3, "chang": 3, "here": 3, "suppos": 4, "TO": [4, 6], "BE": [4, 6], "exampl": [4, 7, 8], "modifi": [4, 6], "IT": 4, "accord": 4, "need": [4, 7, 8], "The": [4, 5, 6, 7, 8], "assum": 4, "you": [4, 7, 8], "sourc": 4, "servic": 4, "promot": 4, "model": 4, "similar": 4, "github": 4, "fork": 4, "pull": 4, "request": 4, "workflow": [4, 7], "true": 4, "like": 4, "gitlab": 4, "bitbucket": 4, "might": 4, "when": 4, "gerrit": 4, "notic": [4, 6], "url": 4, "text": 4, "specif": 4, "terminologi": 4, "merg": [4, 6], "pleas": 4, "make": [4, 5, 7], "sure": 4, "check": 4, "have": [4, 7, 8], "assumpt": 4, "mind": 4, "thing": 4, "accordingli": 4, "provid": [4, 6, 7, 8], "correct": 4, "replac": 4, "bottom": 4, "want": [4, 8], "look": 4, "contributor": 4, "especi": [4, 5, 7], "project": [4, 7], "open": 4, "should": 4, "veri": 4, "templat": 4, "few": [4, 7], "extra": 4, "decid": 4, "includ": [4, 6], "mention": 4, "label": 4, "tracker": 4, "autom": 4, "welcom": 4, "rds2py": [4, 8], "focus": 4, "get": 4, "ani": [4, 6], "potenti": 4, "familiar": 4, "develop": [4, 5], "process": 4, "other": [4, 6], "kind": [4, 6], "appreci": 4, "If": [4, 7, 8], "new": 4, "git": [4, 7], "never": 4, "collabor": 4, "previous": 4, "org": [4, 7], "resourc": 4, "list": 4, "excel": 4, "freecodecamp": 4, "1": [4, 5], "user": 4, "expect": 4, "consider": 4, "reason": 4, "respect": 4, "doubt": 4, "softwar": [4, 6], "foundat": 4, "conduct": 4, "good": 4, "term": 4, "behavior": 4, "guidelin": 4, "experi": 4, "gener": [4, 7], "don": [4, 5, 7], "t": [4, 5, 7], "see": [4, 7], "anyth": 4, "feel": [4, 7, 8], "free": [4, 6, 7, 8], "fire": 4, "forget": 4, "close": 4, "search": [4, 5], "solut": 4, "wa": 4, "alreadi": 4, "problem": 4, "consid": [4, 8], "solv": 4, "inform": [4, 7], "about": 4, "program": 4, "oper": [4, 8], "system": 4, "version": [4, 5], "step": [4, 5, 7], "reproduc": 4, "try": 4, "simplifi": 4, "reproduct": 4, "minim": 4, "still": 4, "illustr": 4, "face": 4, "By": 4, "remov": 4, "factor": 4, "help": [4, 5], "u": 4, "identifi": 4, "root": 4, "caus": 4, "doc": 4, "them": 4, "readabl": 4, "coher": 4, "miss": 4, "mistak": 4, "its": 4, "main": 4, "mean": 4, "kept": 4, "same": [4, 5, 7], "done": 4, "wai": 4, "which": 4, "markup": 4, "languag": 4, "restructuredtext": 4, "commonmark": 4, "extens": 4, "host": 4, "follow": [4, 6], "tip": 4, "web": 4, "quick": 4, "propos": 4, "file": [4, 5, 6, 7], "mechan": 4, "tricki": 4, "normal": 4, "work": 4, "perfectli": 4, "fine": 4, "quit": 4, "handi": [4, 7, 8], "interest": 4, "out": [4, 6], "navig": 4, "folder": 4, "find": 4, "would": [4, 7], "click": 4, "littl": 4, "pencil": 4, "icon": 4, "top": 4, "editor": 4, "onc": [4, 8], "finish": 4, "edit": 4, "write": 4, "messag": 4, "form": 4, "page": [4, 5], "describ": 4, "made": 4, "what": 4, "motiv": 4, "behind": 4, "local": 4, "machin": 4, "tox": [4, 7], "built": 4, "server": 4, "preview": 4, "browser": 4, "http": [4, 7], "localhost": 4, "8000": 4, "python3": 4, "m": 4, "directori": [4, 7], "_build": 4, "html": 4, "explan": 4, "intern": 4, "architectur": 4, "descript": 4, "design": 4, "principl": 4, "least": 4, "summari": 4, "concept": 4, "easi": 4, "start": 4, "quickli": 4, "non": 4, "trivial": 4, "best": 4, "first": [4, 7, 8], "discuss": 4, "subject": [4, 6], "often": 4, "avoid": 4, "unnecessari": 4, "we": [4, 5, 7, 8], "recommend": 4, "isol": 4, "virtual": 4, "instal": 4, "easili": [4, 8], "via": 4, "either": [4, 8], "virtualenv": 4, "path": 4, "venv": 4, "bin": 4, "activ": 4, "miniconda": 4, "conda": 4, "n": 4, "3": [4, 5], "six": 4, "pytest": 4, "cov": 4, "account": 4, "do": [4, 6, 7, 8], "button": 4, "copi": [4, 5, 6, 7], "under": 4, "disk": 4, "yourlogin": 4, "cd": 4, "pip": [4, 5, 7], "setuptool": 4, "abl": 4, "import": [4, 7, 8], "repl": 4, "item": 4, "come": 4, "lot": 4, "hook": 4, "automat": 4, "being": 4, "written": 4, "branch": 4, "hold": [4, 7], "checkout": [4, 7], "b": 4, "my": 4, "class": [4, 7], "thei": 4, "public": 4, "api": 4, "yourself": 4, "author": [4, 5, 6], "rst": 4, "re": 4, "record": 4, "valid": 4, "eventu": 4, "compat": 4, "unit": 4, "test": [4, 7, 8], "just": 4, "bugfix": 4, "moreov": 4, "highli": 4, "histori": 4, "log": 4, "graph": 4, "decor": 4, "pretti": 4, "onelin": 4, "abbrev": 4, "recur": 4, "commun": 4, "pattern": 4, "break": 4, "after": 4, "pipx": 4, "sever": 4, "av": 4, "avail": [4, 7, 8], "everyth": 4, "push": 4, "remot": 4, "origin": 4, "go": 4, "send": [4, 8], "review": 4, "uncom": 4, "paragraph": 4, "detail": [4, 7], "pr": [4, 8], "draft": 4, "mark": 4, "readi": 4, "feedback": 4, "continu": 4, "integr": 4, "ci": 4, "requir": 4, "build": [4, 7], "fetch": 4, "tag": 4, "upstream": 4, "command": 4, "0": [4, 5], "return": [4, 8], "script": 4, "egg": 4, "complet": 4, "well": [4, 8], "info": 4, "src": [4, 7], "txt": 4, "recreat": 4, "r": [4, 7, 8], "flag": 4, "For": [4, 7], "reliabl": 4, "7": 4, "OR": [4, 6], "troubl": 4, "weird": 4, "error": 4, "upon": 4, "dedic": 4, "binari": 4, "freshli": 4, "drop": 4, "interact": 4, "session": 4, "occur": 4, "order": 4, "pass": 4, "pdb": 4, "option": 4, "k": 4, "name": 4, "OF": [4, 6], "THE": [4, 6], "fall": 4, "breakpoint": 4, "manual": 4, "section": 4, "pypi": [4, 5, 7], "publicli": 4, "differ": 4, "index": [4, 5], "instruct": 4, "group": 4, "permiss": [4, 6], "success": 4, "current": 4, "v1": 4, "2": [4, 5], "clean": 4, "up": [4, 7], "dist": 4, "rm": 4, "rf": 4, "confus": 4, "old": 4, "dirti": 4, "hash": 4, "size": 4, "distribut": [4, 6], "too": 4, "big": 4, "500kb": 4, "unwant": 4, "clutter": 4, "accident": 4, "publish": [4, 5, 6, 7], "upload": 4, "correctli": 4, "definit": 4, "even": 4, "though": 4, "focu": 4, "idea": 4, "collect": 4, "appli": 4, "sort": 4, "compani": 4, "proprietari": 4, "pars": [5, 7, 8], "extract": 5, "creat": [5, 8], "represent": [5, 7], "dataset": [5, 7], "store": [5, 7, 8], "rd": [5, 7], "It": [5, 8], "support": [5, 7, 8], "bioconductor": [5, 7, 8], "summarizedexperi": [5, 7], "singlecellexperi": [5, 7], "possibl": [5, 7], "becaus": [5, 7], "aaron": [5, 7], "rds2cpp": [5, 7], "librari": [5, 7], "memori": [5, 7, 8], "view": [5, 7, 8], "except": [5, 7], "string": [5, 7], "so": [5, 6, 7], "access": [5, 7], "c": [5, 6, 7], "space": [5, 8], "through": [5, 7], "cython": [5, 7], "cours": [5, 7], "larg": [5, 7], "data": [5, 7, 8], "overview": 5, "usag": 5, "note": [5, 8], "tutori": 5, "read": 5, "contribut": 5, "issu": 5, "report": 5, "improv": 5, "maintain": 5, "licens": 5, "changelog": 5, "mit": 6, "copyright": 6, "2022": 6, "genentech": 6, "inc": 6, "herebi": 6, "grant": 6, "charg": 6, "person": 6, "obtain": 6, "associ": 6, "deal": 6, "without": 6, "restrict": 6, "limit": 6, "right": 6, "sublicens": 6, "sell": 6, "permit": 6, "whom": 6, "furnish": 6, "condit": 6, "abov": 6, "shall": 6, "substanti": 6, "portion": 6, "AS": 6, "warranti": 6, "express": 6, "impli": 6, "BUT": 6, "NOT": 6, "merchant": 6, "fit": 6, "FOR": 6, "particular": 6, "purpos": 6, "AND": 6, "noninfring": 6, "IN": 6, "NO": 6, "event": 6, "holder": 6, "liabl": 6, "claim": 6, "damag": 6, "liabil": 6, "whether": 6, "an": [6, 7, 8], "action": 6, "contract": 6, "tort": 6, "otherwis": 6, "aris": 6, "connect": 6, "WITH": 6, "construct": [7, 8], "s4": 7, "multipl": 7, "download": [7, 8], "singl": [7, 8], "cell": [7, 8], "as_summarized_experi": [7, 8], "read_rd": [7, 8], "r_obj": 7, "path_to_fil": [7, 8], "dictionari": [7, 8], "transform": 7, "robj": [7, 8], "alwai": 7, "contain": [7, 8], "two": [7, 8], "kei": [7, 8], "atom": [7, 8], "entiti": [7, 8], "numpi": [7, 8], "arrai": 7, "attribut": [7, 8], "convert": [7, 8], "as_spase_matrix": [7, 8], "robject": [7, 8], "spars": [7, 8], "matrix": [7, 8], "sp_mat": [7, 8], "as_spars": 7, "sce": [7, 8], "frame": [7, 8], "dgcmatrix": [7, 8], "dgrmatrix": [7, 8], "dgtmatrix": [7, 8], "bind": 7, "initi": 7, "extern": 7, "cmake": 7, "bytem": 7, "share": 7, "core": 7, "py": 7, "build_ext": 7, "inplac": 7, "typic": 7, "set": 7, "4": 7, "5": 7, "explor": 8, "realiz": 8, "structur": 8, "friendli": 8, "dens": 8, "dim": 8, "as_dense_matrix": 8, "as_sparse_matrix": 8, "dense_mat": 8, "dframe": 8, "as_panda": 8, "df": 8, "how": 8, "serv": 8, "complex": 8, "thats": 8, "hack": 8, "encapsul": 8}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"rds2py": [0, 1, 5, 7], "packag": 1, "submodul": 1, "interfac": 1, "modul": 1, "parser": 1, "pdf": 1, "content": [1, 5], "contributor": 2, "changelog": 3, "version": 3, "0": 3, "3": 3, "develop": [3, 7], "1": [3, 8], "todo": 4, "contribut": 4, "issu": 4, "report": 4, "document": 4, "improv": 4, "code": 4, "submit": 4, "an": 4, "creat": 4, "environ": 4, "clone": 4, "repositori": 4, "implement": 4, "your": 4, "chang": 4, "troubleshoot": 4, "maintain": 4, "task": 4, "releas": 4, "instal": [5, 7], "indic": 5, "tabl": 5, "licens": 6, "usag": 7, "note": 7, "tutori": 8, "step": 8, "read": 8, "rd": 8, "file": 8, "python": 8, "2": 8, "represent": 8, "matric": 8, "panda": 8, "datafram": 8, "s4": 8, "class": 8, "specif": 8, "singlecellexperi": 8, "summarizedexperi": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"rds2py": [[0, "rds2py"], [5, "rds2py"], [7, "rds2py"]], "rds2py package": [[1, "rds2py-package"]], "Submodules": [[1, "submodules"]], "rds2py.interface module": [[1, "rds2py-interface-module"]], "rds2py.parser module": [[1, "rds2py-parser-module"]], "rds2py.pdf module": [[1, "rds2py-pdf-module"]], "Module contents": [[1, "module-contents"]], "Contributors": [[2, "contributors"]], "Changelog": [[3, "changelog"]], "Version 0.3.0 (development)": [[3, "version-0-3-0-development"]], "Version 0.1": [[3, "version-0-1"]], "Todo": [[4, "id1"], [4, "id2"], [4, "id3"], [4, "id5"], [4, "id6"], [4, "id7"], [4, "id8"], [4, "id9"], [4, "id10"], [4, "id11"], [4, "id12"]], "Contributing": [[4, "contributing"]], "Issue Reports": [[4, "issue-reports"]], "Documentation Improvements": [[4, "documentation-improvements"]], "Code Contributions": [[4, "code-contributions"]], "Submit an issue": [[4, "submit-an-issue"]], "Create an environment": [[4, "create-an-environment"]], "Clone the repository": [[4, "clone-the-repository"]], "Implement your changes": [[4, "implement-your-changes"]], "Submit your contribution": [[4, "submit-your-contribution"]], "Troubleshooting": [[4, "troubleshooting"]], "Maintainer tasks": [[4, "maintainer-tasks"]], "Releases": [[4, "releases"]], "Install": [[5, "install"], [7, "install"]], "Contents": [[5, "contents"]], "Indices and tables": [[5, "indices-and-tables"]], "License": [[6, "license"]], "Usage": [[7, "usage"]], "Developer Notes": [[7, "developer-notes"]], "Note": [[7, "note"]], "Tutorial": [[8, "tutorial"]], "Step 1: Read a RDS file in Python": [[8, "step-1-read-a-rds-file-in-python"]], "Step 2: Python representations": [[8, "step-2-python-representations"]], "Matrices": [[8, "matrices"]], "Pandas DataFrame": [[8, "pandas-dataframe"]], "S4 classes: specifically SingleCellExperiment or SummarizedExperiment": [[8, "s4-classes-specifically-singlecellexperiment-or-summarizedexperiment"]]}, "indexentries": {}})
\ No newline at end of file
+Search.setIndex({"docnames": ["api/modules", "api/rds2py", "authors", "changelog", "contributing", "index", "license", "readme", "tutorial"], "filenames": ["api/modules.rst", "api/rds2py.rst", "authors.md", "changelog.md", "contributing.md", "index.md", "license.md", "readme.md", "tutorial.md"], "titles": ["rds2py", "rds2py package", "Contributors", "Changelog", "Contributing", "rds2py", "License", "rds2py", "Tutorial"], "terms": {"packag": [0, 3, 4, 5, 7, 8], "submodul": [0, 7], "grang": 0, "modul": [0, 4, 5], "interfac": [0, 4], "parser": [0, 3], "pdf": 0, "content": [0, 4], "jkanch": 2, "jayaram": 2, "kancherla": 2, "gmail": 2, "com": [2, 4], "thi": [3, 4, 5, 6, 7, 8], "releas": 3, "migrat": 3, "more": [3, 4, 7, 8], "palat": 3, "googl": 3, "": [3, 4, 5, 7], "python": [3, 4, 5, 7], "style": [3, 4], "guid": [3, 4], "A": [3, 6], "major": [3, 4], "modif": 3, "i": [3, 4, 5, 6, 7, 8], "case": [3, 4], "all": [3, 4, 6], "camelcas": 3, "properti": [3, 7, 8], "method": [3, 4, 8], "function": [3, 4, 7, 8], "paramet": 3, "ar": [3, 4, 8], "now": [3, 7, 8], "snake_cas": 3, "In": [3, 4, 7], "addit": [3, 4, 7, 8], "docstr": [3, 4], "document": [3, 5, 6, 7], "ha": [3, 7], "been": [3, 4, 7], "updat": [3, 4], "us": [3, 4, 5, 6, 7, 8], "sphinx": [3, 4], "featur": [3, 4], "link": [3, 4], "object": [3, 5, 7, 8], "type": 3, "also": [3, 4, 8], "privat": [3, 4], "special": 3, "dunder": 3, "e": [3, 4], "g": [3, 4], "__getitem__": 3, "__copy__": 3, "etc": 3, "intersphinx": 3, "refer": [3, 4, 5], "from": [3, 4, 5, 6, 7, 8], "depend": [3, 4, 7], "configur": [3, 4], "flake8": [3, 4], "ruff": 3, "black": [3, 4], "ad": [3, 4], "pyproject": 3, "toml": 3, "setup": [3, 4, 7], "cfg": [3, 4], "less": 3, "annoi": 3, "final": 3, "pyscaffold": [3, 4, 7], "myst": [3, 4], "markdown": 3, "compil": [3, 4], "instead": [3, 4], "recommonmark": 3, "As": 3, "part": [3, 4], "one": [3, 4, 7, 8], "mai": [3, 4], "pre": [3, 4], "commit": [3, 4], "run": [3, 4, 7], "some": [3, 8], "routin": 3, "task": [3, 5], "lint": 3, "format": 3, "befor": [3, 4], "everi": 3, "while": [3, 4], "sometim": [3, 4], "can": [3, 4, 5, 7, 8], "ignor": 3, "verifi": 3, "bring": 3, "consist": 3, "code": [3, 5], "base": [3, 4, 7, 8], "fix": [3, 4], "nasti": 3, "bug": [3, 4], "1729": 3, "add": [3, 4, 8], "your": 3, "chang": 3, "here": 3, "suppos": 4, "TO": [4, 6], "BE": [4, 6], "exampl": [4, 7, 8], "modifi": [4, 6], "IT": 4, "accord": 4, "need": [4, 7, 8], "The": [4, 5, 6, 7, 8], "assum": 4, "you": [4, 7, 8], "sourc": 4, "servic": 4, "promot": 4, "model": 4, "similar": 4, "github": 4, "fork": 4, "pull": 4, "request": 4, "workflow": [4, 7], "true": 4, "like": 4, "gitlab": 4, "bitbucket": 4, "might": 4, "when": 4, "gerrit": 4, "notic": [4, 6], "url": 4, "text": 4, "specif": 4, "terminologi": 4, "merg": [4, 6], "pleas": 4, "make": [4, 5, 7], "sure": 4, "check": 4, "have": [4, 7, 8], "assumpt": 4, "mind": 4, "thing": 4, "accordingli": 4, "provid": [4, 6, 7, 8], "correct": 4, "replac": 4, "bottom": 4, "want": [4, 8], "look": 4, "contributor": 4, "especi": [4, 5, 7], "project": [4, 7], "open": 4, "should": 4, "veri": 4, "templat": 4, "few": [4, 7], "extra": 4, "decid": 4, "includ": [4, 6], "mention": 4, "label": 4, "tracker": 4, "autom": 4, "welcom": 4, "rds2py": [4, 8], "focus": 4, "get": 4, "ani": [4, 6], "potenti": 4, "familiar": 4, "develop": [4, 5], "process": 4, "other": [4, 6], "kind": [4, 6], "appreci": 4, "If": [4, 7, 8], "new": 4, "git": [4, 7], "never": 4, "collabor": 4, "previous": 4, "org": [4, 7], "resourc": 4, "list": 4, "excel": 4, "freecodecamp": 4, "1": [4, 5], "user": 4, "expect": 4, "consider": 4, "reason": 4, "respect": 4, "doubt": 4, "softwar": [4, 6], "foundat": 4, "conduct": 4, "good": 4, "term": 4, "behavior": 4, "guidelin": 4, "experi": 4, "gener": [4, 7], "don": [4, 5, 7], "t": [4, 5, 7], "see": [4, 7], "anyth": 4, "feel": [4, 7, 8], "free": [4, 6, 7, 8], "fire": 4, "forget": 4, "close": 4, "search": [4, 5], "solut": 4, "wa": 4, "alreadi": 4, "problem": 4, "consid": [4, 8], "solv": 4, "inform": [4, 7], "about": 4, "program": 4, "oper": [4, 8], "system": 4, "version": [4, 5], "step": [4, 5, 7], "reproduc": 4, "try": 4, "simplifi": 4, "reproduct": 4, "minim": 4, "still": 4, "illustr": 4, "face": 4, "By": 4, "remov": 4, "factor": 4, "help": [4, 5], "u": 4, "identifi": 4, "root": 4, "caus": 4, "doc": 4, "them": 4, "readabl": 4, "coher": 4, "miss": 4, "mistak": 4, "its": 4, "main": 4, "mean": 4, "kept": 4, "same": [4, 5, 7], "done": 4, "wai": 4, "which": 4, "markup": 4, "languag": 4, "restructuredtext": 4, "commonmark": 4, "extens": 4, "host": 4, "follow": [4, 6], "tip": 4, "web": 4, "quick": 4, "propos": 4, "file": [4, 5, 6, 7], "mechan": 4, "tricki": 4, "normal": 4, "work": 4, "perfectli": 4, "fine": 4, "quit": 4, "handi": [4, 7, 8], "interest": 4, "out": [4, 6], "navig": 4, "folder": 4, "find": 4, "would": [4, 7], "click": 4, "littl": 4, "pencil": 4, "icon": 4, "top": 4, "editor": 4, "onc": [4, 8], "finish": 4, "edit": 4, "write": 4, "messag": 4, "form": 4, "page": [4, 5], "describ": 4, "made": 4, "what": 4, "motiv": 4, "behind": 4, "local": 4, "machin": 4, "tox": [4, 7], "built": 4, "server": 4, "preview": 4, "browser": 4, "http": [4, 7], "localhost": 4, "8000": 4, "python3": 4, "m": 4, "directori": [4, 7], "_build": 4, "html": 4, "explan": 4, "intern": 4, "architectur": 4, "descript": 4, "design": 4, "principl": 4, "least": 4, "summari": 4, "concept": 4, "easi": 4, "start": 4, "quickli": 4, "non": 4, "trivial": 4, "best": 4, "first": [4, 7, 8], "discuss": 4, "subject": [4, 6], "often": 4, "avoid": 4, "unnecessari": 4, "we": [4, 5, 7, 8], "recommend": 4, "isol": 4, "virtual": 4, "instal": 4, "easili": [4, 8], "via": 4, "either": [4, 8], "virtualenv": 4, "path": 4, "venv": 4, "bin": 4, "activ": 4, "miniconda": 4, "conda": 4, "n": 4, "3": [4, 5], "six": 4, "pytest": 4, "cov": 4, "account": 4, "do": [4, 6, 7, 8], "button": 4, "copi": [4, 5, 6, 7], "under": 4, "disk": 4, "yourlogin": 4, "cd": 4, "pip": [4, 5, 7], "setuptool": 4, "abl": 4, "import": [4, 7, 8], "repl": 4, "item": 4, "come": 4, "lot": 4, "hook": 4, "automat": 4, "being": 4, "written": 4, "branch": 4, "hold": [4, 7], "checkout": [4, 7], "b": 4, "my": 4, "class": [4, 7], "thei": 4, "public": 4, "api": 4, "yourself": 4, "author": [4, 5, 6], "rst": 4, "re": 4, "record": 4, "valid": 4, "eventu": 4, "compat": 4, "unit": 4, "test": [4, 7, 8], "just": 4, "bugfix": 4, "moreov": 4, "highli": 4, "histori": 4, "log": 4, "graph": 4, "decor": 4, "pretti": 4, "onelin": 4, "abbrev": 4, "recur": 4, "commun": 4, "pattern": 4, "break": 4, "after": 4, "pipx": 4, "sever": 4, "av": 4, "avail": [4, 7, 8], "everyth": 4, "push": 4, "remot": 4, "origin": 4, "go": 4, "send": [4, 8], "review": 4, "uncom": 4, "paragraph": 4, "detail": [4, 7], "pr": [4, 8], "draft": 4, "mark": 4, "readi": 4, "feedback": 4, "continu": 4, "integr": 4, "ci": 4, "requir": 4, "build": [4, 7], "fetch": 4, "tag": 4, "upstream": 4, "command": 4, "0": [4, 5], "return": [4, 8], "script": 4, "egg": 4, "complet": 4, "well": [4, 8], "info": 4, "src": [4, 7], "txt": 4, "recreat": 4, "r": [4, 7, 8], "flag": 4, "For": [4, 7], "reliabl": 4, "7": 4, "OR": [4, 6], "troubl": 4, "weird": 4, "error": 4, "upon": 4, "dedic": 4, "binari": 4, "freshli": 4, "drop": 4, "interact": 4, "session": 4, "occur": 4, "order": 4, "pass": 4, "pdb": 4, "option": 4, "k": 4, "name": 4, "OF": [4, 6], "THE": [4, 6], "fall": 4, "breakpoint": 4, "manual": 4, "section": 4, "pypi": [4, 5, 7], "publicli": 4, "differ": 4, "index": [4, 5], "instruct": 4, "group": 4, "permiss": [4, 6], "success": 4, "current": 4, "v1": 4, "2": [4, 5], "clean": 4, "up": [4, 7], "dist": 4, "rm": 4, "rf": 4, "confus": 4, "old": 4, "dirti": 4, "hash": 4, "size": 4, "distribut": [4, 6], "too": 4, "big": 4, "500kb": 4, "unwant": 4, "clutter": 4, "accident": 4, "publish": [4, 5, 6, 7], "upload": 4, "correctli": 4, "definit": 4, "even": 4, "though": 4, "focu": 4, "idea": 4, "collect": 4, "appli": 4, "sort": 4, "compani": 4, "proprietari": 4, "pars": [5, 7, 8], "extract": 5, "creat": [5, 8], "represent": [5, 7], "dataset": [5, 7], "store": [5, 7, 8], "rd": [5, 7], "It": [5, 8], "support": [5, 7, 8], "bioconductor": [5, 7, 8], "summarizedexperi": [5, 7], "singlecellexperi": [5, 7], "possibl": [5, 7], "becaus": [5, 7], "aaron": [5, 7], "rds2cpp": [5, 7], "librari": [5, 7], "memori": [5, 7, 8], "view": [5, 7, 8], "except": [5, 7], "string": [5, 7], "so": [5, 6, 7], "access": [5, 7], "c": [5, 6, 7], "space": [5, 8], "through": [5, 7], "cython": [5, 7], "cours": [5, 7], "larg": [5, 7], "data": [5, 7, 8], "overview": 5, "usag": 5, "note": [5, 8], "tutori": 5, "read": 5, "contribut": 5, "issu": 5, "report": 5, "improv": 5, "maintain": 5, "licens": 5, "changelog": 5, "mit": 6, "copyright": 6, "2022": 6, "genentech": 6, "inc": 6, "herebi": 6, "grant": 6, "charg": 6, "person": 6, "obtain": 6, "associ": 6, "deal": 6, "without": 6, "restrict": 6, "limit": 6, "right": 6, "sublicens": 6, "sell": 6, "permit": 6, "whom": 6, "furnish": 6, "condit": 6, "abov": 6, "shall": 6, "substanti": 6, "portion": 6, "AS": 6, "warranti": 6, "express": 6, "impli": 6, "BUT": 6, "NOT": 6, "merchant": 6, "fit": 6, "FOR": 6, "particular": 6, "purpos": 6, "AND": 6, "noninfring": 6, "IN": 6, "NO": 6, "event": 6, "holder": 6, "liabl": 6, "claim": 6, "damag": 6, "liabil": 6, "whether": 6, "an": [6, 7, 8], "action": 6, "contract": 6, "tort": 6, "otherwis": 6, "aris": 6, "connect": 6, "WITH": 6, "construct": [7, 8], "s4": 7, "multipl": 7, "download": [7, 8], "singl": [7, 8], "cell": [7, 8], "as_summarized_experi": [7, 8], "read_rd": [7, 8], "r_obj": 7, "path_to_fil": [7, 8], "dictionari": [7, 8], "transform": 7, "robj": [7, 8], "alwai": 7, "contain": [7, 8], "two": [7, 8], "kei": [7, 8], "atom": [7, 8], "entiti": [7, 8], "numpi": [7, 8], "arrai": 7, "attribut": [7, 8], "convert": [7, 8], "as_spase_matrix": [7, 8], "robject": [7, 8], "spars": [7, 8], "matrix": [7, 8], "sp_mat": [7, 8], "as_spars": 7, "sce": [7, 8], "frame": [7, 8], "dgcmatrix": [7, 8], "dgrmatrix": [7, 8], "dgtmatrix": [7, 8], "bind": 7, "initi": 7, "extern": 7, "cmake": 7, "bytem": 7, "share": 7, "core": 7, "py": 7, "build_ext": 7, "inplac": 7, "typic": 7, "set": 7, "4": 7, "5": 7, "explor": 8, "realiz": 8, "structur": 8, "friendli": 8, "dens": 8, "dim": 8, "as_dense_matrix": 8, "as_sparse_matrix": 8, "dense_mat": 8, "dframe": 8, "as_panda": 8, "df": 8, "how": 8, "serv": 8, "complex": 8, "thats": 8, "hack": 8, "encapsul": 8}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"rds2py": [0, 1, 5, 7], "packag": 1, "submodul": 1, "grang": 1, "modul": 1, "interfac": 1, "parser": 1, "pdf": 1, "content": [1, 5], "contributor": 2, "changelog": 3, "version": 3, "0": 3, "3": 3, "develop": [3, 7], "1": [3, 8], "todo": 4, "contribut": 4, "issu": 4, "report": 4, "document": 4, "improv": 4, "code": 4, "submit": 4, "an": 4, "creat": 4, "environ": 4, "clone": 4, "repositori": 4, "implement": 4, "your": 4, "chang": 4, "troubleshoot": 4, "maintain": 4, "task": 4, "releas": 4, "instal": [5, 7], "indic": 5, "tabl": 5, "licens": 6, "usag": 7, "note": 7, "tutori": 8, "step": 8, "read": 8, "rd": 8, "file": 8, "python": 8, "2": 8, "represent": 8, "matric": 8, "panda": 8, "datafram": 8, "s4": 8, "class": 8, "specif": 8, "singlecellexperi": 8, "summarizedexperi": 8}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 60}, "alltitles": {"rds2py": [[0, "rds2py"], [5, "rds2py"], [7, "rds2py"]], "rds2py package": [[1, "rds2py-package"]], "Submodules": [[1, "submodules"]], "rds2py.granges module": [[1, "rds2py-granges-module"]], "rds2py.interface module": [[1, "rds2py-interface-module"]], "rds2py.parser module": [[1, "rds2py-parser-module"]], "rds2py.pdf module": [[1, "rds2py-pdf-module"]], "Module contents": [[1, "module-contents"]], "Contributors": [[2, "contributors"]], "Changelog": [[3, "changelog"]], "Version 0.3.0 (development)": [[3, "version-0-3-0-development"]], "Version 0.1": [[3, "version-0-1"]], "Todo": [[4, "id1"], [4, "id2"], [4, "id3"], [4, "id5"], [4, "id6"], [4, "id7"], [4, "id8"], [4, "id9"], [4, "id10"], [4, "id11"], [4, "id12"]], "Contributing": [[4, "contributing"]], "Issue Reports": [[4, "issue-reports"]], "Documentation Improvements": [[4, "documentation-improvements"]], "Code Contributions": [[4, "code-contributions"]], "Submit an issue": [[4, "submit-an-issue"]], "Create an environment": [[4, "create-an-environment"]], "Clone the repository": [[4, "clone-the-repository"]], "Implement your changes": [[4, "implement-your-changes"]], "Submit your contribution": [[4, "submit-your-contribution"]], "Troubleshooting": [[4, "troubleshooting"]], "Maintainer tasks": [[4, "maintainer-tasks"]], "Releases": [[4, "releases"]], "Install": [[5, "install"], [7, "install"]], "Contents": [[5, "contents"]], "Indices and tables": [[5, "indices-and-tables"]], "License": [[6, "license"]], "Usage": [[7, "usage"]], "Developer Notes": [[7, "developer-notes"]], "Note": [[7, "note"]], "Tutorial": [[8, "tutorial"]], "Step 1: Read a RDS file in Python": [[8, "step-1-read-a-rds-file-in-python"]], "Step 2: Python representations": [[8, "step-2-python-representations"]], "Matrices": [[8, "matrices"]], "Pandas DataFrame": [[8, "pandas-dataframe"]], "S4 classes: specifically SingleCellExperiment or SummarizedExperiment": [[8, "s4-classes-specifically-singlecellexperiment-or-summarizedexperiment"]]}, "indexentries": {}})
\ No newline at end of file