Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial.
The 3 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
- [1] § STAR★Methods › Method details › Two years follow-up ↔ multiqc/templates/default/assets/js/packages/showdown.min.js, the whole file · a weak match · score 0.60 · ping, speech, hearing, walking, national, child
- [2] § STAR★Methods › Quantification and statistical analysis ↔ R/data_sanity_check.R, lines 1–134 · score 0.56 · mia, mixed, taxonomic, pairwise, genus, ANCOM
- [3] § STAR★Methods › Quantification and statistical analysis ↔ multiqc/templates/default/assets/js/packages/plotly-3.1.2.custom.min.js, the whole file · a weak match · score 0.55 · variance, linear, DA, transformation, NY, absolute
Paper
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The authors' code
JavaScript · 3 lines · 73 KB · GPL-3.0 · 1 match
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",dragon_face:"🐲",dress:"👗",dromedary_camel:"🐪",drooling_face:"🤤",droplet:"💧",drum:"🥁",duck:"🦆",dvd:"📀","e-mail":"📧",eagle:"🦅",ear:"👂",ear_of_rice:"🌾",earth_africa:"🌍",earth_americas:"🌎",earth_asia:"🌏",egg:"🥚",eggplant:"🍆",eight_pointed_black_star:"✴️",eight_spoked_asterisk:"✳️",electric_plug:"🔌",elephant:"🐘",email:"✉️",end:"🔚",envelope_with_arrow:"📩",euro:"💶",european_castle:"🏰",european_post_office:"🏤",evergreen_tree:"🌲",exclamation:"❗️",expressionless:"😑",eye:"👁",eye_speech_bubble:"👁‍🗨",eyeglasses:"👓",eyes:"👀",face_with_head_bandage:"🤕",face_with_thermometer:"🤒",fist_oncoming:"👊",factory:"🏭",fallen_leaf:"🍂",family_man_woman_boy:"👪",family_man_boy:"👨‍👦",family_man_boy_boy:"👨‍👦‍👦",family_man_girl:"👨‍👧",family_man_girl_boy:"👨‍👧‍👦",family_man_girl_girl:"👨‍👧‍👧",family_man_man_boy:"👨‍👨‍👦",family_man_man_boy_boy:"👨‍👨‍👦‍👦",family_man_man_girl:"👨‍👨‍👧",family_man_man_girl_boy:"👨‍👨‍👧‍👦",family_man_man_girl_girl:"👨‍👨‍👧‍👧",family_man_woman_boy_boy:"👨‍👩‍👦‍👦",family_man_woman_girl:"👨‍👩‍👧",family_man_woman_girl_boy:"👨‍👩‍👧‍👦",family_man_woman_girl_girl:"👨‍👩‍👧‍👧",family_woman_boy:"👩‍👦",family_woman_boy_boy:"👩‍👦‍👦",family_woman_girl:"👩‍👧",family_woman_girl_boy:"👩‍👧‍👦",family_woman_girl_girl:"👩‍👧‍👧",family_woman_woman_boy:"👩‍👩‍👦",family_woman_woman_boy_boy:"👩‍👩‍👦‍👦",family_woman_woman_girl:"👩‍👩‍👧",family_woman_woman_girl_boy:"👩‍👩‍👧‍👦",family_woman_woman_girl_girl:"👩‍👩‍👧‍👧",fast_forward:"⏩",fax:"📠",fearful:"😨",feet:"🐾",female_detective:"🕵️‍♀️",ferris_wheel:"🎡",ferry:"⛴",field_hockey:"🏑",file_cabinet:"🗄",file_folder:"📁",film_projector:"📽",film_strip:"🎞",fire:"🔥",fire_engine:"🚒",fireworks:"🎆",first_quarter_moon:"🌓",first_quarter_moon_with_face:"🌛",fish:"🐟",fish_cake:"🍥",fishing_pole_and_fish:"🎣",fist_raised:"✊",fist_left:"🤛",fist_right:"🤜",flags:"🎏",flashlight:"🔦",fleur_de_lis:"⚜️",flight_arrival:"🛬",flight_departure:"🛫",floppy_disk:"💾",flower_playing_cards:"🎴",flushed:"😳",fog:"🌫",foggy:"🌁",football:"🏈",footprints:"👣",fork_and_knife:"🍴",fountain:"⛲️",fountain_pen:"🖋",four_leaf_clover:"🍀",fox_face:"🦊",framed_picture:"🖼",free:"🆓",fried_egg:"🍳",fried_shrimp:"🍤",fries:"🍟",frog:"🐸",frowning:"😦",frowning_face:"☹️",frowning_man:"🙍‍♂️",frowning_woman:"🙍",middle_finger:"🖕",fuelpump:"⛽️",full_moon:"🌕",full_moon_with_face:"🌝",funeral_urn:"⚱️",game_die:"🎲",gear:"⚙️",gem:"💎",gemini:"♊️",ghost:"👻",gift:"🎁",gift_heart:"💝",girl:"👧",globe_with_meridians:"🌐",goal_net:"🥅",goat:"🐐",golf:"⛳️",golfing_man:"🏌️",golfing_woman:"🏌️‍♀️",gorilla:"🦍",grapes:"🍇",green_apple:"🍏",green_book:"📗",green_heart:"💚",green_salad:"🥗",grey_exclamation:"❕",grey_question:"❔",grimacing:"😬",grin:"😁",grinning:"😀",guardsman:"💂",guardswoman:"💂‍♀️",guitar:"🎸",gun:"🔫",haircut_woman:"💇",haircut_man:"💇‍♂️",hamburger:"🍔",hammer:"🔨",hammer_and_pick:"⚒",hammer_and_wrench:"🛠",hamster:"🐹",hand:"✋",handbag:"👜",handshake:"🤝",hankey:"💩",hatched_chick:"🐥",hatching_chick:"🐣",headphones:"🎧",hear_no_evil:"🙉",heart:"❤️",heart_decoration:"💟",heart_eyes:"😍",heart_eyes_cat:"😻",heartbeat:"💓",heartpulse:"💗",hearts:"♥️",heavy_check_mark:"✔️",heavy_division_sign:"➗",heavy_dollar_sign:"💲",heavy_heart_exclamation:"❣️",heavy_minus_sign:"➖",heavy_multiplication_x:"✖️",heavy_plus_sign:"➕",helicopter:"🚁",herb:"🌿",hibiscus:"🌺",high_brightness:"🔆",high_heel:"👠",hocho:"🔪",hole:"🕳",honey_pot:"🍯",horse:"🐴",horse_racing:"🏇",hospital:"🏥",hot_pepper:"🌶",hotdog:"🌭",hotel:"🏨",hotsprings:"♨️",hourglass:"⌛️",hourglass_flowing_sand:"⏳",house:"🏠",house_with_garden:"🏡",houses:"🏘",hugs:"🤗",hushed:"😯",ice_cream:"🍨",ice_hockey:"🏒",ice_skate:"⛸",icecream:"🍦",id:"🆔",ideograph_advantage:"🉐",imp:"👿",inbox_tray:"📥",incoming_envelope:"📨",tipping_hand_woman:"💁",information_source:"ℹ️",innocent:"😇",interrobang:"⁉️",iphone:"📱",izakaya_lantern:"🏮",jack_o_lantern:"🎃",japan:"🗾",japanese_castle:"🏯",japanese_goblin:"👺",japanese_ogre:"👹",jeans:"👖",joy:"😂",joy_cat:"😹",joystick:"🕹",kaaba:"🕋",key:"🔑",keyboard:"⌨️",keycap_ten:"🔟",kick_scooter:"🛴",kimono:"👘",kiss:"💋",kissing:"😗",kissing_cat:"😽",kissing_closed_eyes:"😚",kissing_heart:"😘",kissing_smiling_eyes:"😙",kiwi_fruit:"🥝",koala:"🐨",koko:"🈁",label:"🏷",large_blue_circle:"🔵",large_blue_diamond:"🔷",large_orange_diamond:"🔶",last_quarter_moon:"🌗",last_quarter_moon_with_face:"🌜",latin_cross:"✝️",laughing:"😆",leaves:"🍃",ledger:"📒",left_luggage:"🛅",left_right_arrow:"↔️",leftwards_arrow_with_hook:"↩️",lemon:"🍋",leo:"♌️",leopard:"🐆",level_slider:"🎚",libra:"♎️",light_rail:"🚈",link:"🔗",lion:"🦁",lips:"👄",lipstick:"💄",lizard:"🦎",lock:"🔒",lock_with_ink_pen:"🔏",lollipop:"🍭",loop:"➿",loud_sound:"🔊",loudspeaker:"📢",love_hotel:"🏩",love_letter:"💌",low_brightness:"🔅",lying_face:"🤥",m:"Ⓜ️",mag:"🔍",mag_right:"🔎",mahjong:"🀄️",mailbox:"📫",mailbox_closed:"📪",mailbox_with_mail:"📬",mailbox_with_no_mail:"📭",man:"👨",man_artist:"👨‍🎨",man_astronaut:"👨‍🚀",man_cartwheeling:"🤸‍♂️",man_cook:"👨‍🍳",man_dancing:"🕺",man_facepalming:"🤦‍♂️",man_factory_worker:"👨‍🏭",man_farmer:"👨‍🌾",man_firefighter:"👨‍🚒",man_health_worker:"👨‍⚕️",man_in_tuxedo:"🤵",man_judge:"👨‍⚖️",man_juggling:"🤹‍♂️",man_mechanic:"👨‍🔧",man_office_worker:"👨‍💼",man_pilot:"👨‍✈️",man_playing_handball:"🤾‍♂️",man_playing_water_polo:"🤽‍♂️",man_scientist:"👨‍🔬",man_shrugging:"🤷‍♂️",man_singer:"👨‍🎤",man_student:"👨‍🎓",man_teacher:"👨‍🏫",man_technologist:"👨‍💻",man_with_gua_pi_mao:"👲",man_with_turban:"👳",tangerine:"🍊",mans_shoe:"👞",mantelpiece_clock:"🕰",maple_leaf:"🍁",martial_arts_uniform:"🥋",mask:"😷",massage_woman:"💆",massage_man:"💆‍♂️",meat_on_bone:"🍖",medal_military:"🎖",medal_sports:"🏅",mega:"📣",melon:"🍈",memo:"📝",men_wrestling:"🤼‍♂️",menorah:"🕎",mens:"🚹",metal:"🤘",metro:"🚇",microphone:"🎤",microscope:"🔬",milk_glass:"🥛",milky_way:"🌌",minibus:"🚐",minidisc:"💽",mobile_phone_off:"📴",money_mouth_face:"🤑",money_with_wings:"💸",moneybag:"💰",monkey:"🐒",monkey_face:"🐵",monorail:"🚝",moon:"🌔",mortar_board:"🎓",mosque:"🕌",motor_boat:"🛥",motor_scooter:"🛵",motorcycle:"🏍",motorway:"🛣",mount_fuji:"🗻",mountain:"⛰",mountain_biking_man:"🚵",mountain_biking_woman:"🚵‍♀️",mountain_cableway:"🚠",mountain_railway:"🚞",mountain_snow:"🏔",mouse:"🐭",mouse2:"🐁",movie_camera:"🎥",moyai:"🗿",mrs_claus:"🤶",muscle:"💪",mushroom:"🍄",musical_keyboard:"🎹",musical_note:"🎵",musical_score:"🎼",mute:"🔇",nail_care:"💅",name_badge:"📛",national_park:"🏞",nauseated_face:"🤢",necktie:"👔",negative_squared_cross_mark:"❎",nerd_face:"🤓",neutral_face:"😐",new:"🆕",new_moon:"🌑",new_moon_with_face:"🌚",newspaper:"📰",newspaper_roll:"🗞",next_track_button:"⏭",ng:"🆖",no_good_man:"🙅‍♂️",no_good_woman:"🙅",night_with_stars:"🌃",no_bell:"🔕",no_bicycles:"🚳",no_entry:"⛔️",no_entry_sign:"🚫",no_mobile_phones:"📵",no_mouth:"😶",no_pedestrians:"🚷",no_smoking:"🚭","non-potable_water":"🚱",nose:"👃",notebook:"📓",notebook_with_decorative_cover:"📔",notes:"🎶",nut_and_bolt:"🔩",o:"⭕️",o2:"🅾️",ocean:"🌊",octopus:"🐙",oden:"🍢",office:"🏢",oil_drum:"🛢",ok:"🆗",ok_hand:"👌",ok_man:"🙆‍♂️",ok_woman:"🙆",old_key:"🗝",older_man:"👴",older_woman:"👵",om:"🕉",on:"🔛",oncoming_automobile:"🚘",oncoming_bus:"🚍",oncoming_police_car:"🚔",oncoming_taxi:"🚖",open_file_folder:"📂",open_hands:"👐",open_mouth:"😮",open_umbrella:"☂️",ophiuchus:"⛎",orange_book:"📙",orthodox_cross:"☦️",outbox_tray:"📤",owl:"🦉",ox:"🐂",package:"📦",page_facing_up:"📄",page_with_curl:"📃",pager:"📟",paintbrush:"🖌",palm_tree:"🌴",pancakes:"🥞",panda_face:"🐼",paperclip:"📎",paperclips:"🖇",parasol_on_ground:"⛱",parking:"🅿️",part_alternation_mark:"〽️",partly_sunny:"⛅️",passenger_ship:"🛳",passport_control:"🛂",pause_button:"⏸",peace_symbol:"☮️",peach:"🍑",peanuts:"🥜",pear:"🍐",pen:"🖊",pencil2:"✏️",penguin:"🐧",pensive:"😔",performing_arts:"🎭",persevere:"😣",person_fencing:"🤺",pouting_woman:"🙎",phone:"☎️",pick:"⛏",pig:"🐷",pig2:"🐖",pig_nose:"🐽",pill:"💊",pineapple:"🍍",ping_pong:"🏓",pisces:"♓️",pizza:"🍕",place_of_worship:"🛐",plate_with_cutlery:"🍽",play_or_pause_button:"⏯",point_down:"👇",point_left:"👈",point_right:"👉",point_up:"☝️",point_up_2:"👆",police_car:"🚓",policewoman:"👮‍♀️",poodle:"🐩",popcorn:"🍿",post_office:"🏣",postal_horn:"📯",postbox:"📮",potable_water:"🚰",potato:"🥔",pouch:"👝",poultry_leg:"🍗",pound:"💷",rage:"😡",pouting_cat:"😾",pouting_man:"🙎‍♂️",pray:"🙏",prayer_beads:"📿",pregnant_woman:"🤰",previous_track_button:"⏮",prince:"🤴",princess:"👸",printer:"🖨",purple_heart:"💜",purse:"👛",pushpin:"📌",put_litter_in_its_place:"🚮",question:"❓",rabbit:"🐰",rabbit2:"🐇",racehorse:"🐎",racing_car:"🏎",radio:"📻",radio_button:"🔘",radioactive:"☢️",railway_car:"🚃",railway_track:"🛤",rainbow:"🌈",rainbow_flag:"🏳️‍🌈",raised_back_of_hand:"🤚",raised_hand_with_fingers_splayed:"🖐",raised_hands:"🙌",raising_hand_woman:"🙋",raising_hand_man:"🙋‍♂️",ram:"🐏",ramen:"🍜",rat:"🐀",record_button:"⏺",recycle:"♻️",red_circle:"🔴",registered:"®️",relaxed:"☺️",relieved:"😌",reminder_ribbon:"🎗",repeat:"🔁",repeat_one:"🔂",rescue_worker_helmet:"⛑",restroom:"🚻",revolving_hearts:"💞",rewind:"⏪",rhinoceros:"🦏",ribbon:"🎀",rice:"🍚",rice_ball:"🍙",rice_cracker:"🍘",rice_scene:"🎑",right_anger_bubble:"🗯",ring:"💍",robot:"🤖",rocket:"🚀",rofl:"🤣",roll_eyes:"🙄",roller_coaster:"🎢",rooster:"🐓",rose:"🌹",rosette:"🏵",rotating_light:"🚨",round_pushpin:"📍",rowing_man:"🚣",rowing_woman:"🚣‍♀️",rugby_football:"🏉",running_man:"🏃",running_shirt_with_sash:"🎽",running_woman:"🏃‍♀️",sa:"🈂️",sagittarius:"♐️",sake:"🍶",sandal:"👡",santa:"🎅",satellite:"📡",saxophone:"🎷",school:"🏫",school_satchel:"🎒",scissors:"✂️",scorpion:"🦂",scorpius:"♏️",scream:"😱",scream_cat:"🙀",scroll:"📜",seat:"💺",secret:"㊙️",see_no_evil:"🙈",seedling:"🌱",selfie:"🤳",shallow_pan_of_food:"🥘",shamrock:"☘️",shark:"🦈",shaved_ice:"🍧",sheep:"🐑",shell:"🐚",shield:"🛡",shinto_shrine:"⛩",ship:"🚢",shirt:"👕",shopping:"🛍",shopping_cart:"🛒",shower:"🚿",shrimp:"🦐",signal_strength:"📶",six_pointed_star:"🔯",ski:"🎿",skier:"⛷",skull:"💀",skull_and_crossbones:"☠️",sleeping:"😴",sleeping_bed:"🛌",sleepy:"😪",slightly_frowning_face:"🙁",slightly_smiling_face:"🙂",slot_machine:"🎰",small_airplane:"🛩",small_blue_diamond:"🔹",small_orange_diamond:"🔸",small_red_triangle:"🔺",small_red_triangle_down:"🔻",smile:"😄",smile_cat:"😸",smiley:"😃",smiley_cat:"😺",smiling_imp:"😈",smirk:"😏",smirk_cat:"😼",smoking:"🚬",snail:"🐌",snake:"🐍",sneezing_face:"🤧",snowboarder:"🏂",snowflake:"❄️",snowman:"⛄️",snowman_with_snow:"☃️",sob:"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showdown.min.js at commit dc565eb, under GPL-3.0 · at the source
Overview
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Crown Princess Victoria Children’s Hospital, University Hospital, Linköping, Sweden
- Clinical Department of Pediatrics, Vrinnevi Hospital, Norrköping, Sweden
- Department of Bioscience, University of Vic – Central University of Catalonia, Vic, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central (IRIS-CC), Vic, Spain
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
Abstract
Preterm birth is associated with a high risk of long-term neurological deficits. Although research underscores the role of the gut microbiome in the gut-brain axis, the mechanisms of neurodevelopmental impairment remain elusive. In this prospective observational study (PROPEL), we evaluated whether early gut microbiota development and Limosilactobacillus reuteri supplementation to extremely preterm infants with extremely low birth weight (EPT-ELBW) are associated with neurodevelopment at 2 years. Gut microbiota was characterized by 16S sequencing, and neurodevelopment was assessed by Bayley-III score. Microbiota composition constellations and lower microbial diversity, but not single bacteria, are associated with impaired neurodevelopment. Microbial maturation over the first month was discriminative for motor development, with higher abundance of E. coli and Enterococcus relative to Cutibacterium associated with impairment. L. reuteri supplementation did not seem to affect neurodevelopment via the gut microbiome. In conclusion, dynamics of gut microbiota maturation during early life may impact neurodevelopment in EPT-ELBW infants.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repositories
Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.
magge30/PROPEL-2y-neurodevelopment
3d1b337f65a0fd2c2b39cc3b20ee59d529aa63b9, 3 February 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
9 files
- ANCOM-BC.R, R, 58 lines
- Alpha-diversity.R, R, 125 lines
- Beta-diversity.R, R, 52 lines
- Functions.R, R, 47 lines
- Longitudinal_analysis.R, R, 131 lines
- PLS-DA.R, R, 111 lines
- SparceMCMM.R, R, 20 lines
- libraries.R, R, 21 lines
- README.md, Text, 24 lines
ewels/MultiQC
dc565eb9eef7b22a289ab7eec78e5efb6bf297c3, 28 September 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
725 files
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modules/ , Python, 1 linefgumi/ tests/ __init__.py - multiqc/
modules/ , Python, 45 linesfgumi/ tests/ conftest.py - multiqc/
modules/ , Python, 103 linesfgumi/ tests/ test_commands.py - multiqc/
modules/ , Python, 121 linesfgumi/ tests/ test_consensus_families. py - multiqc/
modules/ , Python, 59 linesfgumi/ tests/ test_consensus_stats.py - multiqc/
modules/ , Python, 118 linesfgumi/ tests/ test_contract.py - multiqc/
modules/ , Python, 86 linesfgumi/ tests/ test_dedup.py - multiqc/
modules/ , Python, 202 linesfgumi/ tests/ test_family_sizes.py - multiqc/
modules/ , Python, 23 linesfgumi/ tests/ test_grouping.py - multiqc/
modules/ , Python, 11 linesfgumi/ tests/ test_review.py - multiqc/
modules/ , Python, 58 linesfgumi/ tests/ test_schemas.py - multiqc/
modules/ , Python, 87 linesfgumi/ tests/ test_umis.py - multiqc/
modules/ , Python, 40 linesfgumi/ tests/ test_yields.py - multiqc/
modules/ , Python, 168 linesfgumi/ umis.py - multiqc/
modules/ , Python, 220 linesfgumi/ util.py - multiqc/
modules/ , Python, 122 linesfgumi/ yields.py - multiqc/
modules/ , Python, 3 linesfiltlong/ __init__.py - multiqc/
modules/ , Python, 108 linesfiltlong/ filtlong.py - multiqc/
modules/ , Python, 3 linesflash/ __init__.py - multiqc/
modules/ , Python, 300 linesflash/ flash.py - multiqc/
modules/ , Python, 3 linesflexbar/ __init__.py - multiqc/
modules/ , Python, 133 linesflexbar/ flexbar.py - multiqc/
modules/ , Python, 3 linesfreyja/ __init__.py - multiqc/
modules/ , Python, 140 linesfreyja/ freyja.py - multiqc/
modules/ , Python, 3 linesganon/ __init__.py - multiqc/
modules/ , Python, 343 linesganon/ ganon.py - multiqc/
modules/ , Python, 3 linesgatk/ __init__.py - multiqc/
modules/ , Python, 409 linesgatk/ analyze_saturation_mutag enesis.py - multiqc/
modules/ , Python, 223 linesgatk/ base_recalibrator.py - multiqc/
modules/ , Python, 69 linesgatk/ gatk.py - multiqc/
modules/ , Python, 48 linesgatk/ utils.py - multiqc/
modules/ , Python, 268 linesgatk/ varianteval.py - multiqc/
modules/ , Python, 3 linesgffcompare/ __init__.py - multiqc/
modules/ , Python, 280 linesgffcompare/ gffcompare.py - multiqc/
modules/ , Python, 3 linesglimpse/ __init__.py - multiqc/
modules/ , Python, 220 linesglimpse/ err_grp.py - multiqc/
modules/ , Python, 294 linesglimpse/ err_spl.py - multiqc/
modules/ , Python, 45 linesglimpse/ glimpse.py - multiqc/
modules/ , Python, 3 linesgoleft_indexcov/ __init__.py - multiqc/
modules/ , Python, 237 linesgoleft_indexcov/ goleft_indexcov.py - multiqc/
modules/ , Python, 3 linesgopeaks/ __init__.py - multiqc/
modules/ , Python, 112 linesgopeaks/ gopeaks.py - multiqc/
modules/ , Python, 3 linesgtdbtk/ __init__.py - multiqc/
modules/ , Python, 192 linesgtdbtk/ gtdbtk.py - multiqc/
modules/ , Python, 3 lineshaplocheck/ __init__.py - multiqc/
modules/ , Python, 112 lineshaplocheck/ haplocheck.py - multiqc/
modules/ , Python, 3 lineshappy/ __init__.py - multiqc/
modules/ , Python, 293 lineshappy/ happy.py - multiqc/
modules/ , Python, 3 lineshicexplorer/ __init__.py - multiqc/
modules/ , Python, 338 lineshicexplorer/ hicexplorer.py - multiqc/
modules/ , Python, 3 lineshicpro/ __init__.py - multiqc/
modules/ , Python, 487 lineshicpro/ hicpro.py - multiqc/
modules/ , Python, 3 lineshicstuff/ __init__.py - multiqc/
modules/ , Python, 363 lineshicstuff/ hicstuff.py - multiqc/
modules/ , Python, 3 lineshicup/ __init__.py - multiqc/
modules/ , Python, 279 lineshicup/ hicup.py - multiqc/
modules/ , Python, 3 lineshifi_trimmer/ __init__.py - multiqc/
modules/ , Python, 293 lineshifi_trimmer/ hifi_trimmer.py - multiqc/
modules/ , Python, 3 lineshifiasm/ __init__.py - multiqc/
modules/ , Python, 109 lineshifiasm/ hifiasm.py - multiqc/
modules/ , Python, 3 lineshisat2/ __init__.py - multiqc/
modules/ , Python, 186 lineshisat2/ hisat2.py - multiqc/
modules/ , Python, 3 lineshomer/ __init__.py - multiqc/
modules/ , Python, 82 lineshomer/ findpeaks.py - multiqc/
modules/ , Python, 76 lineshomer/ homer.py - multiqc/
modules/ , Python, 480 lineshomer/ tagdirectory.py - multiqc/
modules/ , Python, 3 lineshops/ __init__.py - multiqc/
modules/ , Python, 150 lineshops/ hops.py - multiqc/
modules/ , Python, 3 lineshostile/ __init__.py - multiqc/
modules/ , Python, 142 lineshostile/ hostile.py - multiqc/
modules/ , Python, 3 lineshtseq/ __init__.py - multiqc/
modules/ , Python, 136 lineshtseq/ htseq.py - multiqc/
modules/ , Python, 3 lineshumid/ __init__.py - multiqc/
modules/ , Python, 63 lineshumid/ clusters.py - multiqc/
modules/ , Python, 64 lineshumid/ counts.py - multiqc/
modules/ , Python, 46 lineshumid/ humid.py - multiqc/
modules/ , Python, 63 lineshumid/ neighbours.py - multiqc/
modules/ , Python, 130 lineshumid/ stats.py - multiqc/
modules/ , Python, 3 linesinterop/ __init__.py - multiqc/
modules/ , Python, 493 linesinterop/ interop.py - multiqc/
modules/ , Python, 3 linesisoseq/ __init__.py - multiqc/
modules/ , Python, 261 linesisoseq/ isoseq.py - multiqc/
modules/ , Python, 3 linesivar/ __init__.py - multiqc/
modules/ , Python, 177 linesivar/ ivar.py - multiqc/
modules/ , Python, 3 linesjcvi/ __init__.py - multiqc/
modules/ , Python, 373 linesjcvi/ jcvi.py - multiqc/
modules/ , Python, 3 linesjellyfish/ __init__.py - multiqc/
modules/ , Python, 122 linesjellyfish/ jellyfish.py - multiqc/
modules/ , Python, 3 lineskaiju/ __init__.py - multiqc/
modules/ , Python, 301 lineskaiju/ kaiju.py - multiqc/
modules/ , Python, 3 lineskallisto/ __init__.py - multiqc/
modules/ , Python, 147 lineskallisto/ kallisto.py - multiqc/
modules/ , Python, 3 lineskat/ __init__.py - multiqc/
modules/ , Python, 116 lineskat/ kat.py - multiqc/
modules/ , Python, 3 lineskraken/ __init__.py - multiqc/
modules/ , Python, 470 lineskraken/ kraken.py - multiqc/
modules/ , Python, 3 linesleehom/ __init__.py - multiqc/
modules/ , Python, 96 linesleehom/ leehom.py - multiqc/
modules/ , Python, 3 lineslibrarian/ __init__.py - multiqc/
modules/ , Python, 186 lineslibrarian/ librarian.py - multiqc/
modules/ , Python, 3 lineslima/ __init__.py - multiqc/
modules/ , Python, 366 lineslima/ lima.py - multiqc/
modules/ , Python, 3 lineslongranger/ __init__.py - multiqc/
modules/ , Python, 427 lineslongranger/ longranger.py - multiqc/
modules/ , Python, 3 linesmacs2/ __init__.py - multiqc/
modules/ , Python, 160 linesmacs2/ macs2.py - multiqc/
modules/ , Python, 3 linesmalt/ __init__.py - multiqc/
modules/ , Python, 192 linesmalt/ malt.py - multiqc/
modules/ , Python, 3 linesmapdamage/ __init__.py - multiqc/
modules/ , Python, 291 linesmapdamage/ mapdamage.py - multiqc/
modules/ , Python, 3 linesmegahit/ __init__.py - multiqc/
modules/ , Python, 147 linesmegahit/ megahit.py - multiqc/
modules/ , Python, 3 linesmetaphlan/ __init__.py - multiqc/
modules/ , Python, 341 linesmetaphlan/ metaphlan.py - multiqc/
modules/ , Python, 3 linesmethurator/ __init__.py - multiqc/
modules/ , Python, 370 linesmethurator/ methurator.py - multiqc/
modules/ , Python, 3 linesmethylqa/ __init__.py - multiqc/
modules/ , Python, 129 linesmethylqa/ methylqa.py - multiqc/
modules/ , Python, 3 linesmgikit/ __init__.py - multiqc/
modules/ , Python, 507 linesmgikit/ mgikit.py - multiqc/
modules/ , Python, 3 linesmgnifam/ __init__.py - multiqc/
modules/ , Python, 330 linesmgnifam/ mgnifam.py - multiqc/
modules/ , Python, 1 linemgnifam/ tests/ __init__.py - multiqc/
modules/ , Python, 163 linesmgnifam/ tests/ test_mgnifam.py - multiqc/
modules/ , Python, 3 linesminionqc/ __init__.py - multiqc/
modules/ , Python, 263 linesminionqc/ minionqc.py - multiqc/
modules/ , Python, 3 linesmirtop/ __init__.py - multiqc/
modules/ , Python, 260 linesmirtop/ mirtop.py - multiqc/
modules/ , Python, 3 linesmirtrace/ __init__.py - multiqc/
modules/ , Python, 369 linesmirtrace/ mirtrace.py - multiqc/
modules/ , Python, 3 linesmosaicatcher/ __init__.py - multiqc/
modules/ , Python, 175 linesmosaicatcher/ mosaicatcher.py - multiqc/
modules/ , Python, 3 linesmosdepth/ __init__.py - multiqc/
modules/ , Python, 609 linesmosdepth/ mosdepth.py - multiqc/
modules/ , Python, 1 linemosdepth/ tests/ __init__.py - multiqc/
modules/ , Python, 21 linesmosdepth/ tests/ test_gen_stats.py - multiqc/
modules/ , Python, 59 linesmosdepth/ tests/ test_xy_coverage.py - multiqc/
modules/ , Python, 3 linesmotus/ __init__.py - multiqc/
modules/ , Python, 252 linesmotus/ motus.py - multiqc/
modules/ , Python, 3 linesmtnucratio/ __init__.py - multiqc/
modules/ , Python, 114 linesmtnucratio/ mtnucratio.py - multiqc/
modules/ , Python, 3 linesmultivcfanalyzer/ __init__.py - multiqc/
modules/ , Python, 290 linesmultivcfanalyzer/ multivcfanalyzer.py - multiqc/
modules/ , Python, 3 linesnanoq/ __init__.py - multiqc/
modules/ , Python, 321 linesnanoq/ nanoq.py - multiqc/
modules/ , Python, 3 linesnanostat/ __init__.py - multiqc/
modules/ , Python, 486 linesnanostat/ nanostat.py - multiqc/
modules/ , Python, 3 linesnextclade/ __init__.py - multiqc/
modules/ , Python, 321 linesnextclade/ nextclade.py - multiqc/
modules/ , Python, 3 linesngsbits/ __init__.py - multiqc/
modules/ , Python, 196 linesngsbits/ mappingqc.py - multiqc/
modules/ , Python, 47 linesngsbits/ ngsbits.py - multiqc/
modules/ , Python, 176 linesngsbits/ readqc.py - multiqc/
modules/ , Python, 111 linesngsbits/ samplegender.py - multiqc/
modules/ , Python, 28 linesngsbits/ utils.py - multiqc/
modules/ , Python, 3 linesngsderive/ __init__.py - multiqc/
modules/ , Python, 474 linesngsderive/ ngsderive.py - multiqc/
modules/ , Python, 3 linesnonpareil/ __init__.py - multiqc/
modules/ , Python, 404 linesnonpareil/ nonpareil.py - multiqc/
modules/ , Python, 3 linesodgi/ __init__.py - multiqc/
modules/ , Python, 470 linesodgi/ odgi.py - multiqc/
modules/ , Python, 3 linesoptitype/ __init__.py - multiqc/
modules/ , Python, 140 linesoptitype/ optitype.py - multiqc/
modules/ , Python, 3 linespairtools/ __init__.py - multiqc/
modules/ , Python, 346 linespairtools/ pairtools.py - multiqc/
modules/ , Python, 276 linespairtools/ utils.py - multiqc/
modules/ , Python, 3 linespangolin/ __init__.py - multiqc/
modules/ , Python, 259 linespangolin/ pangolin.py - multiqc/
modules/ , Python, 3 linespbmarkdup/ __init__.py - multiqc/
modules/ , Python, 141 linespbmarkdup/ pbmarkdup.py - multiqc/
modules/ , Python, 3 linespeddy/ __init__.py - multiqc/
modules/ , Python, 348 linespeddy/ peddy.py - multiqc/
modules/ , Python, 3 linespercolator/ __init__.py - multiqc/
modules/ , Python, 118 linespercolator/ percolator.py - multiqc/
modules/ , Python, 3 linesphantompeakqualtools/ __init__.py - multiqc/
modules/ , Python, 93 linesphantompeakqualtools/ phantompeakqualtools.py - multiqc/
modules/ , Python, 160 linespicard/ AlignmentSummaryMetrics. py - multiqc/
modules/ , Python, 167 linespicard/ BaseDistributionByCycleM etrics.py - multiqc/
modules/ , Python, 390 linespicard/ CrosscheckFingerprints.p y - multiqc/
modules/ , Python, 168 linespicard/ ExtractIlluminaBarcodes. py - multiqc/
modules/ , Python, 143 linespicard/ GcBiasMetrics.py - multiqc/
modules/ , Python, 439 linespicard/ HsMetrics.py - multiqc/
modules/ , Python, 126 linespicard/ IlluminaBasecallingMetri cs.py - multiqc/
modules/ , Python, 122 linespicard/ IlluminaLaneMetrics.py - multiqc/
modules/ , Python, 205 linespicard/ InsertSizeMetrics.py - multiqc/
modules/ , Python, 325 linespicard/ MarkDuplicates.py - multiqc/
modules/ , Python, 64 linespicard/ MarkIlluminaAdapters.py - multiqc/
modules/ , Python, 105 linespicard/ OxoGMetrics.py - multiqc/
modules/ , Python, 171 linespicard/ QualityByCycleMetrics.py - multiqc/
modules/ , Python, 60 linespicard/ QualityScoreDistribution Metrics.py - multiqc/
modules/ , Python, 93 linespicard/ QualityYieldMetrics.py - multiqc/
modules/ , Python, 213 linespicard/ RnaSeqMetrics.py - multiqc/
modules/ , Python, 165 linespicard/ RrbsSummaryMetrics.py - multiqc/
modules/ , Python, 147 linespicard/ TargetedPcrMetrics.py - multiqc/
modules/ , Python, 345 linespicard/ ValidateSamFile.py - multiqc/
modules/ , Python, 406 linespicard/ VariantCallingMetrics.py - multiqc/
modules/ , Python, 240 linespicard/ WgsMetrics.py - multiqc/
modules/ , Python, 3 linespicard/ __init__.py - multiqc/
modules/ , Python, 312 linespicard/ picard.py - multiqc/
modules/ , Python, 1 linepicard/ tests/ __init__.py - multiqc/
modules/ , Python, 54 linespicard/ tests/ test_picard.py - multiqc/
modules/ , Python, 190 linespicard/ util.py - multiqc/
modules/ , Python, 3 linesporechop/ __init__.py - multiqc/
modules/ , Python, 286 linesporechop/ porechop.py - multiqc/
modules/ , Python, 3 linespreseq/ __init__.py - multiqc/
modules/ , Python, 489 linespreseq/ preseq.py - multiqc/
modules/ , Python, 3 linesprinseqplusplus/ __init__.py - multiqc/
modules/ , Python, 143 linesprinseqplusplus/ prinseqplusplus.py - multiqc/
modules/ , Python, 3 linesprokka/ __init__.py - multiqc/
modules/ , Python, 249 linesprokka/ prokka.py - multiqc/
modules/ , Python, 3 linespurple/ __init__.py - multiqc/
modules/ , Python, 225 linespurple/ purple.py - multiqc/
modules/ , Python, 3 linespychopper/ __init__.py - multiqc/
modules/ , Python, 200 linespychopper/ pychopper.py - multiqc/
modules/ , Python, 3 linespycoqc/ __init__.py - multiqc/
modules/ , Python, 325 linespycoqc/ pycoqc.py - multiqc/
modules/ , Python, 3 linesqc3C/ __init__.py - multiqc/
modules/ , Python, 1,025 linesqc3C/ qc3C.py - multiqc/
modules/ , Python, 3 linesqorts/ __init__.py - multiqc/
modules/ , Python, 315 linesqorts/ qorts.py - multiqc/
modules/ , Python, 765 linesqualimap/ QM_BamQC.py - multiqc/
modules/ , Python, 301 linesqualimap/ QM_RNASeq.py - multiqc/
modules/ , Python, 115 linesqualimap/ __init__.py - multiqc/
modules/ , Python, 78 linesqualimap/ qualimap.py - multiqc/
modules/ , Python, 3 linesquast/ __init__.py - multiqc/
modules/ , Python, 409 linesquast/ quast.py - multiqc/
modules/ , Python, 3 linesribodetector/ __init__.py - multiqc/
modules/ , Python, 162 linesribodetector/ ribodetector.py - multiqc/
modules/ , Python, 3 linesribotish/ __init__.py - multiqc/
modules/ , Python, 479 linesribotish/ ribotish.py - multiqc/
modules/ , Python, 1 lineribotish/ tests/ __init__.py - multiqc/
modules/ , Python, 214 linesribotish/ tests/ test_ribotish.py - multiqc/
modules/ , Python, 3 linesribowaltz/ __init__.py - multiqc/
modules/ , Python, 561 linesribowaltz/ ribowaltz.py - multiqc/
modules/ , Python, 3 linesriker/ __init__.py - multiqc/
modules/ , Python, 288 linesriker/ alignment.py - multiqc/
modules/ , Python, 215 linesriker/ basic.py - multiqc/
modules/ , Python, 132 linesriker/ gcbias.py - multiqc/
modules/ , Python, 385 linesriker/ hybcap.py - multiqc/
modules/ , Python, 152 linesriker/ isize.py - multiqc/
modules/ , Python, 69 linesriker/ riker.py - multiqc/
modules/ , Python, 1 lineriker/ tests/ __init__.py - multiqc/
modules/ , Python, 320 linesriker/ tests/ test_riker.py - multiqc/
modules/ , Python, 59 linesriker/ util.py - multiqc/
modules/ , Python, 372 linesriker/ wgs.py - multiqc/
modules/ , Python, 3 linesrna_seqc/ __init__.py - multiqc/
modules/ , Python, 431 linesrna_seqc/ rna_seqc.py - multiqc/
modules/ , Python, 3 linesrockhopper/ __init__.py - multiqc/
modules/ , Python, 206 linesrockhopper/ rockhopper.py - multiqc/
modules/ , Python, 3 linesrsem/ __init__.py - multiqc/
modules/ , Python, 187 linesrsem/ rsem.py - multiqc/
modules/ , Python, 3 linesrseqc/ __init__.py - multiqc/
modules/ , Python, 138 linesrseqc/ bam_stat.py - multiqc/
modules/ , Python, 123 linesrseqc/ gene_body_coverage.py - multiqc/
modules/ , Python, 90 linesrseqc/ infer_experiment.py - multiqc/
modules/ , Python, 81 linesrseqc/ inner_distance.py - multiqc/
modules/ , Python, 105 linesrseqc/ junction_annotation.py - multiqc/
modules/ , Python, 90 linesrseqc/ junction_saturation.py - multiqc/
modules/ , Python, 145 linesrseqc/ read_distribution.py - multiqc/
modules/ , Python, 67 linesrseqc/ read_duplication.py - multiqc/
modules/ , Python, 80 linesrseqc/ read_gc.py - multiqc/
modules/ , Python, 92 linesrseqc/ rseqc.py - multiqc/
modules/ , Python, 66 linesrseqc/ tin.py - multiqc/
modules/ , Python, 3 linessalmon/ __init__.py - multiqc/
modules/ , Python, 155 linessalmon/ salmon.py - multiqc/
modules/ , Python, 3 linessambamba/ __init__.py - multiqc/
modules/ , Python, 170 linessambamba/ markdup.py - multiqc/
modules/ , Python, 71 linessambamba/ sambamba.py - multiqc/
modules/ , Python, 3 linessamblaster/ __init__.py - multiqc/
modules/ , Python, 122 linessamblaster/ samblaster.py - multiqc/
modules/ , Python, 3 linessamtools/ __init__.py - multiqc/
modules/ , Python, 215 linessamtools/ ampliconclip.py - multiqc/
modules/ , Python, 297 linessamtools/ coverage.py - multiqc/
modules/ , Python, 203 linessamtools/ flagstat.py - multiqc/
modules/ , Python, 175 linessamtools/ idxstats.py - multiqc/
modules/ , Python, 189 linessamtools/ markdup.py - multiqc/
modules/ , Python, 86 linessamtools/ rmdup.py - multiqc/
modules/ , Python, 170 linessamtools/ samtools.py - multiqc/
modules/ , Python, 317 linessamtools/ stats.py - multiqc/
modules/ , Python, 1 linesamtools/ tests/ __init__.py - multiqc/
modules/ , Python, 82 linessamtools/ tests/ test_coverage.py - multiqc/
modules/ , Python, 126 linessamtools/ tests/ test_flagstat.py - multiqc/
modules/ , Python, 3 linessargasso/ __init__.py - multiqc/
modules/ , Python, 153 linessargasso/ sargasso.py - multiqc/
modules/ , Python, 3 linesseqera_cli/ __init__.py - multiqc/
modules/ , Python, 411 linesseqera_cli/ seqera_cli.py - multiqc/
modules/ , Python, 3 linesseqfu/ __init__.py - multiqc/
modules/ , Python, 52 linesseqfu/ seqfu.py - multiqc/
modules/ , Python, 300 linesseqfu/ stats.py - multiqc/
modules/ , Python, 70 linesseqfu/ test/ test_stats.py - multiqc/
modules/ , Python, 3 linesseqkit/ __init__.py - multiqc/
modules/ , Python, 57 linesseqkit/ seqkit.py - multiqc/
modules/ , Python, 316 linesseqkit/ stats.py - multiqc/
modules/ , Python, 1 lineseqkit/ tests/ __init__.py - multiqc/
modules/ , Python, 148 linesseqkit/ tests/ test_stats.py - multiqc/
modules/ , Python, 3 linessequali/ __init__.py - multiqc/
modules/ , Python, 928 linessequali/ sequali.py - multiqc/
modules/ , Python, 3 linesseqwho/ __init__.py - multiqc/
modules/ , Python, 262 linesseqwho/ seqwho.py - multiqc/
modules/ , Python, 3 linesseqyclean/ __init__.py - multiqc/
modules/ , Python, 177 linesseqyclean/ seqyclean.py - multiqc/
modules/ , Python, 3 linessexdeterrmine/ __init__.py - multiqc/
modules/ , Python, 179 linessexdeterrmine/ sexdeterrmine.py - multiqc/
modules/ , Python, 3 linessickle/ __init__.py - multiqc/
modules/ , Python, 132 linessickle/ sickle.py - multiqc/
modules/ , Python, 3 linessincei/ __init__.py - multiqc/
modules/ , Python, 15 linessincei/ _helpers.py - multiqc/
modules/ , Python, 180 linessincei/ scCountQC.py - multiqc/
modules/ , Python, 263 linessincei/ scFilterStats.py - multiqc/
modules/ , Python, 71 linessincei/ sincei.py - multiqc/
modules/ , Python, 3 linesskewer/ __init__.py - multiqc/
modules/ , Python, 157 linesskewer/ skewer.py - multiqc/
modules/ , Python, 3 linesslamdunk/ __init__.py - multiqc/
modules/ , Python, 621 linesslamdunk/ slamdunk.py - multiqc/
modules/ , Python, 3 linessnippy/ __init__.py - multiqc/
modules/ , Python, 263 linessnippy/ snippy.py - multiqc/
modules/ , Python, 3 linessnpeff/ __init__.py - multiqc/
modules/ , Python, 359 linessnpeff/ snpeff.py - multiqc/
modules/ , Python, 3 linessnpsplit/ __init__.py - multiqc/
modules/ , Python, 292 linessnpsplit/ snpsplit.py - multiqc/
modules/ , Python, 3 linessomalier/ __init__.py - multiqc/
modules/ , Python, 719 linessomalier/ somalier.py - multiqc/
modules/ , Python, 3 linessompy/ __init__.py - multiqc/
modules/ , Python, 206 linessompy/ sompy.py - multiqc/
modules/ , Python, 3 linessortmerna/ __init__.py - multiqc/
modules/ , Python, 164 linessortmerna/ sortmerna.py - multiqc/
modules/ , Python, 3 linessourmash/ __init__.py - multiqc/
modules/ , Python, 81 linessourmash/ compare.py - multiqc/
modules/ , Python, 219 linessourmash/ gather.py - multiqc/
modules/ , Python, 56 linessourmash/ sourmash.py - multiqc/
modules/ , Python, 3 linesspaceranger/ __init__.py - multiqc/
modules/ , Python, 348 linesspaceranger/ count.py - multiqc/
modules/ , Python, 47 linesspaceranger/ spaceranger.py - multiqc/
modules/ , Python, 81 linesspaceranger/ utils.py - multiqc/
modules/ , Python, 3 linesstacks/ __init__.py - multiqc/
modules/ , Python, 301 linesstacks/ stacks.py - multiqc/
modules/ , Python, 3 linesstar/ __init__.py - multiqc/
modules/ , Python, 413 linesstar/ star.py - multiqc/
modules/ , Python, 3 linessupernova/ __init__.py - multiqc/
modules/ , Python, 550 linessupernova/ supernova.py - multiqc/
modules/ , Python, 3 linessylphtax/ __init__.py - multiqc/
modules/ , Python, 360 linessylphtax/ sylphtax.py - multiqc/
modules/ , Python, 3 linestelseq/ __init__.py - multiqc/
modules/ , Python, 85 linestelseq/ telseq.py - multiqc/
modules/ , Python, 3 linestheta2/ __init__.py - multiqc/
modules/ , Python, 106 linestheta2/ theta2.py - multiqc/
modules/ , Python, 3 linestophat/ __init__.py - multiqc/
modules/ , Python, 144 linestophat/ tophat.py - multiqc/
modules/ , Python, 3 linestrim_galore/ __init__.py - multiqc/
modules/ , Python, 603 linestrim_galore/ trim_galore.py - multiqc/
modules/ , Python, 3 linestrimmomatic/ __init__.py - multiqc/
modules/ , Python, 169 linestrimmomatic/ trimmomatic.py - multiqc/
modules/ , Python, 3 linestruvari/ __init__.py - multiqc/
modules/ , Python, 307 linestruvari/ truvari.py - multiqc/
modules/ , Python, 3 linesumicollapse/ __init__.py - multiqc/
modules/ , Python, 1 lineumicollapse/ tests/ __init__.py - multiqc/
modules/ , Python, 79 linesumicollapse/ tests/ test_umicollapse.py - multiqc/
modules/ , Python, 220 linesumicollapse/ umicollapse.py - multiqc/
modules/ , Python, 3 linesumitools/ __init__.py - multiqc/
modules/ , Python, 1 lineumitools/ tests/ __init__.py - multiqc/
modules/ , Python, 48 linesumitools/ tests/ test_umitools.py - multiqc/
modules/ , Python, 402 linesumitools/ umitools.py - multiqc/
modules/ , Python, 3 linesvarscan2/ __init__.py - multiqc/
modules/ , Python, 247 linesvarscan2/ varscan2.py - multiqc/
modules/ , Python, 3 linesvcftools/ __init__.py - multiqc/
modules/ , Python, 93 linesvcftools/ relatedness2.py - multiqc/
modules/ , Python, 65 linesvcftools/ tstv_by_count.py - multiqc/
modules/ , Python, 66 linesvcftools/ tstv_by_qual.py - multiqc/
modules/ , Python, 53 linesvcftools/ tstv_summary.py - multiqc/
modules/ , Python, 82 linesvcftools/ vcftools.py - multiqc/
modules/ , Python, 3 linesvep/ __init__.py - multiqc/
modules/ , Python, 405 linesvep/ vep.py - multiqc/
modules/ , Python, 3 linesverifybamid/ __init__.py - multiqc/
modules/ , Python, 355 linesverifybamid/ verifybamid.py - multiqc/
modules/ , Python, 3 linesvg/ __init__.py - multiqc/
modules/ , Python, 314 linesvg/ vg.py - multiqc/
modules/ , Python, 3 lineswhatshap/ __init__.py - multiqc/
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FrederickHuangLin/ANCOMBC
dc4febdf59badb3a8dfe0c767ef2186323c2199a, 18 September 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
28 files
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ancom.R , R, 545 lines - R/
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ancombc2.R , R, 871 lines - R/
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ancombc_mult.R , R, 324 lines - R/
ancombc_prep.R , R, 409 lines - R/
data.R , R, 21 lines - R/
data_sanity_check.R , R, 410 lines, 1 match - R/
secom_dist.R , R, 285 lines - R/
secom_linear.R , R, 330 lines - R/
secom_prep.R , R, 67 lines - R/
sim_data.R , R, 145 lines - R/
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sparse_linear.R , R, 219 lines - R/
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ANCOMBC2.Rmd , R, 1,208 lines - vignettes/
SECOM.Rmd , R, 540 lines - vignettes/
children/ , R, 37 lineschild_atlas1006.Rmd - vignettes/
data_sanity_check.Rmd , R, 175 lines - README.md, Text, 186 lines
chanw0/SparseMCMM
c46959840f9b286b036a3231c2a25d5dd4c28ca2, 28 January 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
14 files
- R/
CausalEffect.R , R, 41 lines - R/
DirechletEstimating.R , R, 61 lines - R/
OutcomeEstimating.R , R, 77 lines - R/
SparseMCMM.R , R, 209 lines - R/
alpha.estimates.R , R, 54 lines - R/
beta.estimates.R , R, 46 lines - R/
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post_selection_inference , R, 172 lines.R - tests/
testthat.R , R, 12 lines - tests/
testthat/ , R, 16 linestest-SparseMCMM.R - LICENSE, License, 2 lines
- LICENSE.md, License, 21 lines
- README.md, Text, 133 lines
thelovelab/tximport
2c532670e2f58139a7ebc3a57fd2ccf22d5b8cdf, 28 September 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
19 files
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alevin.R , R, 296 lines - R/
helper.R , R, 121 lines - R/
infReps.R , R, 132 lines - R/
summarizeToGene.R , R, 184 lines - R/
tximport.R , R, 720 lines - tests/
testthat.R , R, 5 lines - tests/
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testthat/ , R, 41 linestest_h5.R - tests/
testthat/ , R, 63 linestest_inf_reps.R - tests/
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testthat/ , R, 10 linestest_no_tx2gene.R - tests/
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testthat/ , R, 30 linestest_salmon.R - tests/
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tximport.Rmd , R, 521 lines - README.md, Text, 32 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
What the map holds:
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- 787 scripts, each with its path and the digest of its content;
- 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
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Data
No dataset and no data link were found in the paper.
Data and code availability
The 16S rRNA dataset generated in this study is available at the European Nucleotide Archive: PRJEB36531 https://
The anonymized coded data have been made available at https://
All original code has been deposited at https://
Any additional information required to reanalyze the data reported in this study is available from the lead contact upon request.
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 4 keywords, 6 funders, 77 references.
Cite
This paper
Abrahamsson, T., Wejryd, E., Pujolassos, M., Calle, M. L., Sverremark-Ekström, E., Jenmalm, M. C., & Martí, M. (2026). Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial. iScience, 29(5), 115802. https://
BibTeX
@article{abrahamsson2026
author = {Abrahamsson, Thomas and Wejryd, Erik and Pujolassos, Meritxell and Calle, M Luz and Sverremark-Ekström, Eva and Jenmalm, Maria C and Martí, Magalí},
title = {{Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial}},
journal = {iScience},
year = {2026},
month = apr,
volume = {29},
number = {5},
pages = {115802},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/
url = {https://
pmid = {42111202},
pmcid = {PMC13157099}
}
RIS
TY - JOUR
AU - Abrahamsson, Thomas
AU - Wejryd, Erik
AU - Pujolassos, Meritxell
AU - Calle, M Luz
AU - Sverremark-Ekström, Eva
AU - Jenmalm, Maria C
AU - Martí, Magalí
TI - Dynamics of early gut microbiota maturation in extremely preterm infants and neurodevelopment at 2 years of age in a probiotic intervention trial
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/
VL - 29
IS - 5
SP - 115802
SN - 2589-0042
PB - Elsevier
DO - 10.1016/
UR - https://
LA - en
ER -
CSL-JSON
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