- Видео 89
- Просмотров 283 665
Akash Mitra
Индия
Добавлен 11 мар 2017
👨🎓 PhD student
🔬 Muscle biologist
🧑🏻💻 R coding enthusiast
🔬 Muscle biologist
🧑🏻💻 R coding enthusiast
RNAseq analysis using R programming | Part 2 | Running DESeq2 package for analysis | #programming
RNAseq analysis using R programming | Part 2 | Running DESeq2 package for analysis | #programming
Welcome to the second part of our RNA-seq analysis series! In this video, we take a deeper dive into RNA-seq data analysis using DESeq2. You'll learn how to import count data, set up your experimental design, filter low-expression genes, and perform differential expression analysis. We also cover visualizing the results with EnhancedVolcano for easy interpretation of significant genes. Whether you're a beginner or looking to improve your RNA-seq workflow, this tutorial has got you covered!
Airway package: www.bioconductor.org/packages/release/data/experiment/html/airway.html
DESeq2 package: bio...
Welcome to the second part of our RNA-seq analysis series! In this video, we take a deeper dive into RNA-seq data analysis using DESeq2. You'll learn how to import count data, set up your experimental design, filter low-expression genes, and perform differential expression analysis. We also cover visualizing the results with EnhancedVolcano for easy interpretation of significant genes. Whether you're a beginner or looking to improve your RNA-seq workflow, this tutorial has got you covered!
Airway package: www.bioconductor.org/packages/release/data/experiment/html/airway.html
DESeq2 package: bio...
Просмотров: 13
Видео
RNAseq analysis using R programming | Part 1 | Preparation of the data files | #programming
Просмотров 35День назад
Welcome to the first part of our comprehensive tutorial series on RNAseq analysis using R programming! In this video, we’ll guide you through the essential steps to prepare your RNAseq data files for analysis. From downloading required packages to organizing and cleaning your datasets, we’ll cover everything you need to get started on the right foot. Whether you’re a beginner or looking to refi...
How to choose a statistical test | Normally distributed data | Inferential statistics | #howto
Просмотров 1514 дней назад
A short animated video on how you can choose a statistical test. #anova #ttest #chisquaretest #correlation n #regression Subscribe to me Newsletter: akashmitra.substack.com/ 🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸 akash_mitraa 🐤Twitte...
How to use EndNote for adding citations in manuscript| Researcher hacks | Referencing and citations
Просмотров 3921 день назад
EndNote website: endnote.com/ My notion templates for academicians and students: Academic website for students - akashmitra.gumroad.com/l/academic-website-v2 Design portfolio - akashmitra.gumroad.com/l/notion-design-portfolio Academic resume - akashmitra.gumroad.com/l/notion-academic-cv 🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My eboo...
Gene expression analysis using the 'pcr' package in R programming | Coding in biology | R program
Просмотров 139Месяц назад
Link to the github repository: github.com/akashmitraa/R-tutorials.git Playlist of R videos: ruclips.net/video/9YDtD59UUck/видео.html&pp=gAQBiAQB 🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸 akash_mitraa 🐤Twitter - akamitra20 🎵S...
Codon search | #python | Bioinformatics | Looking for codons using basic python codes
Просмотров 2545 месяцев назад
Using basic Python codes including #pythonloops and #conditionals to search for codon position 🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸 akash_mitraa 🐤Twitter - akamitra20 🎵Study with me Playlist - open.spotify.com/playlist/...
Loops in Python programming | while loop | for loop | step by step | for absolute beginners
Просмотров 1305 месяцев назад
🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸 akash_biologist 🐤Twitter - akamitra20 🎵Study with me Playlist - open.spotify.com/playlist/6oN4dUzJJodHPy6acZsfqz Who am I - I am a 2nd Year PhD student working in the field of Muscle...
R programming for biological data analysis | Plotting a bar graph with p-values | Part-4
Просмотров 1369 месяцев назад
🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸Instagram - akash_mitraa 🐤Twitter - akamitra20 🎵Study with me Playlist - open.spotify.com/playlist/6oN4dUzJJodHPy6acZsfqz R programming for biological data analysis | Plotting a bar g...
R programming for biological data analysis | Performing statistical analysis | Part-3
Просмотров 2149 месяцев назад
🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸Instagram - akash_mitraa 🐤Twitter - akamitra20 🎵Study with me Playlist - open.spotify.com/playlist/6oN4dUzJJodHPy6acZsfqz R programming for biological data analysis | Performing stati...
R programming for biological data analysis | Importing dataset and cleaning the data | Part-2
Просмотров 1499 месяцев назад
🕸Website - akashmitraa.github.io/personal-website/ 👨🏻🎓My google scholar profile - shorturl.at/vKX23 📚My ebook database - www.notion.so/Books-for-Biology-e6fe0b4a1aa949c9bf77274224fe12a7 📸Instagram - akash_mitraa 🐤Twitter - akamitra20 🎵Study with me Playlist - open.spotify.com/playlist/6oN4dUzJJodHPy6acZsfqz R programming for biological data analysis | Importing datase...
R programming for biological data analysis | Setting up workspace and installing packages | Part-1
Просмотров 1669 месяцев назад
R programming for biological data analysis | Setting up workspace and installing packages | Part-1
How to set Scale Bar using ImageJ software | Microscope | Imaging #howto #image
Просмотров 23 тыс.Год назад
How to set Scale Bar using ImageJ software | Microscope | Imaging #howto #image
Drawing a Phylogenetic Tree using PYTHON | Biopython tutorial | Bioinformatics
Просмотров 3,7 тыс.Год назад
Drawing a Phylogenetic Tree using PYTHON | Biopython tutorial | Bioinformatics
Pathfinder Academy book review | Life science books | Latest edition
Просмотров 13 тыс.2 года назад
Pathfinder Academy book review | Life science books | Latest edition
#metabolism | Conversion of Pyruvate to Acetyl CoA | PDH Complex | Biochemistry
Просмотров 2 тыс.2 года назад
#metabolism | Conversion of Pyruvate to Acetyl CoA | PDH Complex | Biochemistry
#biopython #python | Sequence Alignment | Bioinformatics | Computational biology
Просмотров 8 тыс.2 года назад
#biopython #python | Sequence Alignment | Bioinformatics | Computational biology
#ChitChat Episode#1 | A chat with Sumona Garg | AIR 74 | CSIR NET 2022 life science qualified
Просмотров 7142 года назад
#ChitChat Episode#1 | A chat with Sumona Garg | AIR 74 | CSIR NET 2022 life science qualified
#Muscles | Anatomy of skeletal muscle | Musculoskeletal system | Physiology and Anatomy
Просмотров 852 года назад
#Muscles | Anatomy of skeletal muscle | Musculoskeletal system | Physiology and Anatomy
#Microbiology | Microbiological Culture Media | Microbiology | Types of media | PART 2
Просмотров 692 года назад
#Microbiology | Microbiological Culture Media | Microbiology | Types of media | PART 2
#Microbiology | Microbiological Culture Media | Microbiology | Types of media | PART 1
Просмотров 1072 года назад
#Microbiology | Microbiological Culture Media | Microbiology | Types of media | PART 1
#Allergy | Type 1 hypersensitivity | Allergic reaction mechanism | Immunology
Просмотров 1272 года назад
#Allergy | Type 1 hypersensitivity | Allergic reaction mechanism | Immunology
#Productivity | How to study better | The S.Q.A.T framework
Просмотров 4052 года назад
#Productivity | How to study better | The S.Q.A.T framework
#Biopython | How to get started | Bioinformatics | Computational biology
Просмотров 28 тыс.2 года назад
#Biopython | How to get started | Bioinformatics | Computational biology
#Biochemistry | Fluorescence Resonance Energy Transfer | FRET
Просмотров 6162 года назад
#Biochemistry | Fluorescence Resonance Energy Transfer | FRET
#Microbiology | How to calculate CFU/ml of bacterial solution | Viable Count Assay
Просмотров 18 тыс.2 года назад
#Microbiology | How to calculate CFU/ml of bacterial solution | Viable Count Assay
#MolecularBiology | Lac operon | PART - 3
Просмотров 812 года назад
#MolecularBiology | Lac operon | PART - 3
#MolecularBiology | Lac operon | PART - 2
Просмотров 512 года назад
#MolecularBiology | Lac operon | PART - 2
#MolecularBiology | Lac operon | PART - 1
Просмотров 1482 года назад
#MolecularBiology | Lac operon | PART - 1
Proteasomal pathway | Protein degradation | Uniquitinylation | Biochemistry | Molecular biology
Просмотров 7463 года назад
Proteasomal pathway | Protein degradation | Uniquitinylation | Biochemistry | Molecular biology
Thank you so much, but If you can tell us how you arrived with the standard measurements that you uploaded or used for the video
Franky, I don’t remember from where I had acquired it. If I get the link, I will put it up on the community post
Thanks Akash Ji....Very Informative Video....
Hi, please make a video about checking quality of data with pca and hierarchical clustering when data is not separate between case and control samples
Sure. I will try to make one in future
@@akashmitrabiologythank you
IDLE gave me this error: Traceback (most recent call last): File "C:/Users/dkb13/OneDrive/Desktop/MC671/python/Prac_1.py", line 2, in <module> for sequence in SeqIO.parse("globin.fasta" , "fasta"): File "C:\Users\dkb13\AppData\Roaming\Python\Python312\site-packages\Bio\SeqIO\__init__.py", line 625, in parse return iterator_generator(handle) File "C:\Users\dkb13\AppData\Roaming\Python\Python312\site-packages\Bio\SeqIO\FastaIO.py", line 187, in __init__ super().__init__(source, mode="t", fmt="Fasta") File "C:\Users\dkb13\AppData\Roaming\Python\Python312\site-packages\Bio\SeqIO\Interfaces.py", line 64, in __init__ self.stream = open(source, "r" + mode) FileNotFoundError: [Errno 2] No such file or directory: 'globin.fasta'
This is wonderful.
Please, I have sent you an email requesting the reference image you used. Thank you.
Hi, thank you for this. I wanted to ask where you are getting the reference image from. Can you provide a reference for the reference image, perhaps somewhere in literature where this has been used? thank you
I actually don’t remember where I found the image. I got the image and checked it against an existing microscopic image with a scale bar that I had. It matched. Hence, I started using it.
That was e great lession ... Thanks a lot sir..... I'm a masters student in microbiology... This video helps me a lot ❤❤❤
I am glad the video could help you!
Nice one 🎉
i got key error with AUG methionine
excusme sir do you have a sample picture at 2:55 but with 400x magnification
Thank you, I am new and the video was really helpful
I am glad it could help
how can we get the reference image?
Please drop me an email at akamitra20@gmail.com
@@akashmitrabiology hello, please send the reference image already drop you an email. Thank you,
Thank you for the video. Can I use the refrence image for inverted microscope images which I took with my mobile camera?
Yes! You can use it.
Thank you. The last question, can I crop my images before adding the scale bar? Or it have effects on the measurements
@@manelialavioun552 you can set the scale according to the uncropped image. After that when you crop it it will adjust according to the aspect ratio
@@akashmitrabiology I've read somewhere that you can crop the image before setting the scale bar, you mean it is wrong? So I have to redo all again.
Thank you for the video. When I insert the scale bar from tools it shows in inches instead of microns, how can I adjust this?
Hi. All you need to do is change the units to um
@@akashmitrabiology I changed in the "set scale" settings, but I don't believe the conversion is correct as it would set scale bars of equal distances for 2 nm and 2um... My image is 1920x1440 pixels.
@@haileydeckers I am unable to understand over this conversation. Could you drop me an email and share your image?
This is gold. Thank so much Sir
Glad it helped!
Thank you Mr Akash, I am new here and have a question Does the resolution of my photomicrograph affect the magnification I would choose on the reference image
I don't think the resolution will be a factor because the magnification won't be affected
Thank you
You're welcome
Thank you!🤩
You’re welcome 😊
Hey, Akash... I have also mailed you. Can you pls check
Hi. Did I reply back to you?
thanks
You're welcome!
Nice explanation, it was verry helpful
Glad to hear that
Hi Akash, thank you for the helpful video! I sent you an email to get the reference image, an you let me know if you received it please? Thank you!
Hi. Did I reply back to you on your email. If not, I am very sorry. Please send me another email.
@@akashmitrabiology Hi! I don't think I received your reply, so I just sent you a new email now. Thank you so much!
Hello sir, grate concept and i love to do biopython and your tutorial is very helpful to learn it . your website is not available, it shows 404 error.
You can check out my website at www.akashmitra.in I think it's running now.
Ha!! You just saved me 🎉❤ I love your class thanks for explaining this topic clearly to me
Glad it helped!
hi sir! kindly send me the reference image. I am greatly in need of it..
Thank you so much sir, your video really help me out🌼
You are most welcome
can i have this image scale bar 1.000x ?
HI. Could you email me at akamitra20@gmail.com? I will send the image
Thank you. Just wondering, why does this reference image work for any type of microscope?
Because whichever microscope you use, 20x or 10x will be universal magnifications. The magnification of 20X in microscope 1 would be same as that of 20X in microscope 2. I hope this answers your question
@@akashmitrabiology please send me the reference image
after hours trying to find about imagej, finally. thank you for this video and the scale bar reference, sir. your audio is so clear, i can immediately understand what you say.
Really appreciate that. Glad I could help
Hello Can we use this reference image (all scales) for all of microscopic images including confocal microscope images?. Thank you
Yes. You can use this for any microscopic images including confocal
Thank you so much sir
You are welcome
Sir iam applying ap pgcet now I'm using this book for studying.
Good luck
Can I use replit?
Yes you can. You have to install the dependencies on replit
@@akashmitrabiology I got No such file or directory: 'tree dnd'. How to upload it on replit?
Hello! I've sent you an email regarding the reference image, sir. Hope that you could address this. Thank you!
I think I emailed you back. Please let me know if I missed it
Hi @jenicaashleypantollana6104, if you received the image, could you also forward it to me please?
Muchas gracias por compartir tu conocimiento, saludos desde Ecuador.
Hi. If I have a protein dataset in fasta file and I wanted to filter them to fish out specific sequences that satisfies few characteristics, how should I do?
Interesting question! I think it’s possible using conditionals. You can check out my codon search video. That might give you some idea. I will have a look as well. Thanks for the idea.
@@akashmitrabiology Thanks. Using conditional helps!
after dragging the main image, i.e., fluorescent image into the imageJ , no dialogue box as such @7:45 appeared for me
It will appear only if you set the scale bar at global in the previous step
@@akashmitrabiology Ya I had set up the scale bar at the prior step but still it is coming like that. Can you please also provide the method of how to count the number of live and dead cells in a image of Live/Dead assay, using ImageJ and that also of a specific RoI (Region of interest) ?
Dear Akash Mitra Sir, I have sent request email for image scale reference. Please kindly need your help. Thank yo Sir
Thanks for sharing the video. I've been struggling with this for a while, but your explanation really helped clear things up!
Do you have a scale reference for 2X?
Unfortunately I don't
Thank you for your kind assistance, sensei. However, I tried making use of the reference scale bar image but it is doubling the actual length of each line I measure.
Thats not possible actually
Hello. I mailed you for the reference image. You haven't replied me. Please address this. I have my thesis defense next month.
Hi. I have sent the image to you
Thank you for this video. I wish PyRx could offer students a special subscription rate for the software, similar to what PyMOL did.
Is PyRx paid nowadays? I haven't used it in a long time though
Amazing explanation ❤
Thanks
How we can know the level of magnification of pictures especially those pictures which are taken through high speed cameras ? Please someone guide me
What about those pictures which we take through camera so how can we know their magnification level ? Please guide
hello sir, how can i get your reference image ?
Drop me an email at akamitra20@gmail.com
Omg thank you sir!!!!!!!
Glad I could help.
tqq bro , it helped me a lot for cell communication elective.
Glad I could help. Please share the videos
@@akashmitrabiology yea sure
Big thanks brother, from Indonesia😊
Glad I could help