Farhan Haq
Farhan Haq
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Відео

miRNA expression analysis using R - Step by step guide
Переглядів 7062 місяці тому
#microRNA #datascience #genome How to perform step by step miRNA expression analysis # Load libraries library(affy) library(affyPLM) library(limma) library(affycomp) library(AgilentQC) # Set working directory to where CEL files are located setwd("E://miRNA/GSE66752_RAW/GSM1631463_179_NS.txt/") data_files - list.files(pattern = "*.txt") data - read.maimages(files = data_files, source = "agilent"...
Download Gene Sequence Using Python -
Переглядів 2503 місяці тому
#python #Biopython #DNA #Gene Following is code I used in the video from Bio import Entrez from Bio import SeqIO # Define the NCBI accession number for the gene you want to download accession_number = "NM_001126114" # Example: Human TP53 gene # Fetch the gene sequence from NCBI with Entrez.efetch(db="nucleotide", id=accession_number, rettype="fasta", retmode="text") as handle: record = SeqIO.re...
Read file in python using function - Code in description
Переглядів 643 місяці тому
#filehandling #reading def read_fasta_sequences(file_path): sequences = [] with open(file_path, 'r') as file: for line in file: line = line.strip() if not line.startswith(' '): sequences.append(line) return sequences # Replace 'your_file.fasta' with the path to your FASTA file file_path = 'your_file.fasta' sequences = read_fasta_sequences(file_path) # Print the sequences for seq in sequences: p...
Reading File In Python - File Handling - L7
Переглядів 855 місяців тому
Reading File In Python - File Handling - L7
Python in Bioinformatics - L6 - Sequences
Переглядів 1196 місяців тому
Python in Bioinformatics - L6 - Sequences
Python in Bioinformatics - L5 - if else elif Nested
Переглядів 5757 місяців тому
Python in Bioinformatics - L5 - if else elif Nested
Python in Bioinformatics - L4 - Logical and Comparison Operators
Переглядів 707 місяців тому
Python in Bioinformatics - L4 - Logical and Comparison Operators
Python in Bioinformatics - L3 - Expressions
Переглядів 1797 місяців тому
Python in Bioinformatics - L3 - Expressions
Python in Bioinformatics - L2 - Datatypes and Variables
Переглядів 987 місяців тому
Python in Bioinformatics - L2 - Datatypes and Variables
Python Basics - Installing Anaconda - Lecture 1
Переглядів 2247 місяців тому
Python Basics - Installing Anaconda - Lecture 1
R and R studio installation - Simple Guide
Переглядів 13810 місяців тому
R and R studio installation - Simple Guide
Correlation with R - simplest tutorial
Переглядів 90611 місяців тому
Correlation with R - simplest tutorial
How to find gene information against a specific probe ID?
Переглядів 453Рік тому
How to find gene information against a specific probe ID?
How to read large text file in windows ?
Переглядів 1,1 тис.Рік тому
How to read large text file in windows ?
JGI Consulting #research #finance #hr
Переглядів 131Рік тому
JGI Consulting #research #finance #hr
Simple Heatmap in R
Переглядів 876Рік тому
Simple Heatmap in R
Gene Set Enrichment Analysis . Simplest guide for biologists
Переглядів 10 тис.Рік тому
Gene Set Enrichment Analysis . Simplest guide for biologists
FASTQ to SAM - WGS Analysis - Step 5
Переглядів 2,2 тис.Рік тому
FASTQ to SAM - WGS Analysis - Step 5
Annotating reference genome for WGS analysis - Step 4
Переглядів 1,9 тис.Рік тому
Annotating reference genome for WGS analysis - Step 4
Download reference genome files for WGS analysis - Step 3
Переглядів 3,7 тис.Рік тому
Download reference genome files for WGS analysis - Step 3
Fastqc - Whole genome sequencing - Step 2
Переглядів 2,6 тис.Рік тому
Fastqc - Whole genome sequencing - Step 2
Download Fastq or SRA files - Whole Genome Sequencing Analysis. Step 1
Переглядів 8 тис.Рік тому
Download Fastq or SRA files - Whole Genome Sequencing Analysis. Step 1
Microarray expression analysis guide for biologists - Very easy and free software -TAC
Переглядів 1,2 тис.2 роки тому
Microarray expression analysis guide for biologists - Very easy and free software -TAC
How to use grep function in linux - Guide for beginners
Переглядів 1782 роки тому
How to use grep function in linux - Guide for beginners
How to make a matrix file for differential expression analysis - Ubuntu
Переглядів 1,2 тис.2 роки тому
How to make a matrix file for differential expression analysis - Ubuntu
How to generate simple Heatmap - R Tutorials
Переглядів 1,3 тис.2 роки тому
How to generate simple Heatmap - R Tutorials
Downloading sequencing data on ubuntu/linux - SRA toolkit
Переглядів 15 тис.2 роки тому
Downloading sequencing data on ubuntu/linux - SRA toolkit
Caculate gene expression with FeatureCounts - Step 7
Переглядів 4,4 тис.2 роки тому
Caculate gene expression with FeatureCounts - Step 7
Indexing BAM file using samtools - Step 6
Переглядів 6 тис.2 роки тому
Indexing BAM file using samtools - Step 6

КОМЕНТАРІ

  • @sreeram6416
    @sreeram6416 6 днів тому

    lots of love and respect to you from INDIA sir

  • @AmandaPorto-u5c
    @AmandaPorto-u5c 12 днів тому

    você me salvouuuuuuu! gratidão <3

  • @hamylerizwan
    @hamylerizwan 16 днів тому

    Cleared everything AGAIN! Jazakallah Khair Sir for uploading it on YT, Dr Hassaan. Got to study this topic again in my MPhil, wanted to revisit and clicked on this video (showing already watched) just to be where I wanted to be, where I got all my concepts in BS.

  • @ShaunelBulao
    @ShaunelBulao 17 днів тому

    Does it require to do this part? 6:10

  • @jyoti2446
    @jyoti2446 19 днів тому

    Thank you sir.......one more request.....can you please make a video on how to install mr.bayers software on windows 🙏☺️

  • @feefaysaltusar1955
    @feefaysaltusar1955 22 дні тому

    How to convert feature count value to FPKM value..

  • @FeeFaysalAhmedDept.OfMathemati

    I want to download genome files of potato. And another problem is which type file will download and how to download. Please help me

    • @FarhanHaqj
      @FarhanHaqj 23 дні тому

      Go to NCBI genome and write the biological name of potato

    • @feefaysaltusar1955
      @feefaysaltusar1955 23 дні тому

      I got a reference genome but which file format download / need for this analysis. I saw your folder (reference genome) many file such as chrLenth.txt, genomeParameter.txt so on.... But i did not get the files... Please suggest me.

    • @feefaysaltusar1955
      @feefaysaltusar1955 23 дні тому

      All the parts you solve easily but a gap here, the files of reference genome folder how to download. You can create a video for this topic. Please

  • @lasthope3498
    @lasthope3498 Місяць тому

    Do you help in assignments?

  • @maheebaloch
    @maheebaloch Місяць тому

    Hello sir , how can I find the sequence of new castle disease virus

    • @FarhanHaqj
      @FarhanHaqj Місяць тому

      You should look it in the genome section of NCBI

  • @Ramya.85
    @Ramya.85 Місяць тому

    thanks sir. better understanding video never saw for complicated sums

  • @Haguynitzan
    @Haguynitzan Місяць тому

    Ruth Nussinov is my grandma(:

  • @sufiyanimran.
    @sufiyanimran. Місяць тому

    dont be Canva artist hire some designers

  • @27b11
    @27b11 Місяць тому

    Thanks very much! This video help my life.

  • @adityakamde3778
    @adityakamde3778 Місяць тому

    Where is this t1.profile file how to generate it please explain

  • @samarthtiku98
    @samarthtiku98 Місяць тому

    Beautiful explaination

  • @prsimoibn2710
    @prsimoibn2710 Місяць тому

    Hello Dr. are the Exiqon LNA Array data , or MicroRNAseq platforms different??

    • @FarhanHaqj
      @FarhanHaqj Місяць тому

      Purpose is same but array data is array chip data while RNAseq is sequencing data.

  • @nivethas9492
    @nivethas9492 Місяць тому

    I have installed R4.3.0 version also, but the packages not showing as not available

    • @FarhanHaqj
      @FarhanHaqj Місяць тому

      Please go to bioconductor for the same command and copy the code

    • @FarhanHaqj
      @FarhanHaqj Місяць тому

      Use BiocManager command to install

  • @nivethas9492
    @nivethas9492 Місяць тому

    expect limma package other packages are not available in the latest version of Rstudio. which version u have used

  • @prsimoibn2710
    @prsimoibn2710 Місяць тому

    I am wondering how to do the annotation. It's really frustrating 😢. I've got DEGs without any column matching my annotation file from johnsnowlabs Also, it seems the AgilentQC package can't be found, so not installed..?

  • @KAVYASINGH-q4i
    @KAVYASINGH-q4i 2 місяці тому

    Very nicely explained

  • @Neha-fi5ik
    @Neha-fi5ik 2 місяці тому

    Can it be downloaded in iPad.

    • @FarhanHaqj
      @FarhanHaqj 2 місяці тому

      You can check. Depends on specifications and OS

  • @amitkarmakar1684
    @amitkarmakar1684 2 місяці тому

    how do you check the quality of the data

    • @FarhanHaqj
      @FarhanHaqj 2 місяці тому

      There are libraries for that. I think something like that agilentqc or affyqc. Depending on the platform

  • @ArnavPadhi
    @ArnavPadhi 2 місяці тому

    please send the link to download the autodoc software

  • @Hussein-ui6bz
    @Hussein-ui6bz 2 місяці тому

    can you provide NGS miRNA differential expression analysis using R studio

  • @madhavanjn
    @madhavanjn 2 місяці тому

    Please post a video on SNP's analysis tools.

  • @madhavanjn
    @madhavanjn 2 місяці тому

    Thank you but how to extract functional SNP's from this file.

  • @scarlettgutierrez6760
    @scarlettgutierrez6760 2 місяці тому

    Thank you very much !! please you can do a video to explain finding best substitution model for phylogenetic analisis in Neibohr joining method . I would appreciate it

  • @Jayesh-w-005
    @Jayesh-w-005 2 місяці тому

    Jay shree ram🚩🧡

  • @namiatakreem9345
    @namiatakreem9345 3 місяці тому

    Where did my got saved, after running all the commands successfully it not in ncbi folder

  • @RutbaMakhdoomi
    @RutbaMakhdoomi 3 місяці тому

    YOU'RE A LITERAL SAVIOURRRR SIR. Thank you for breaking this all down in simpler ways. PS: really appreciate you starting the video with bismillah :)

  • @HtetMyetAung-n9r
    @HtetMyetAung-n9r 3 місяці тому

    I cannot do like your instruction on window 10

  • @sreeram6416
    @sreeram6416 3 місяці тому

    allah bless you with unlimited success sir

  • @duafatima6283
    @duafatima6283 3 місяці тому

    Hi,Thanks for the video but I'm having an error as '--receptor' is not recognized as an internal or external command, operable program or batch file', can you please guide me what's wrong?

  • @rakshithm1257
    @rakshithm1257 3 місяці тому

    What happened to this initiative? Is it still on?

  • @kaythimya3890
    @kaythimya3890 3 місяці тому

    Thank you so much for your valuable informatic video.

  • @kakarlapakeeraiah2580
    @kakarlapakeeraiah2580 3 місяці тому

    I have java latest version and i downloaded ligplus also but it is not installing can you please help me

  • @ابراهيمابراهيم-ت7ظ
    @ابراهيمابراهيم-ت7ظ 3 місяці тому

    ❤❤❤

  • @ابراهيمابراهيم-ت7ظ
    @ابراهيمابراهيم-ت7ظ 3 місяці тому

    الكعبة روحي

  • @sandrajose7452
    @sandrajose7452 3 місяці тому

    Hello Dr. Farhan, do you have a follow up of this tutorial? Thank you so much for all the tutorials that you shared with the scientific community!

    • @FarhanHaqj
      @FarhanHaqj 3 місяці тому

      No. Actually, its very straightforward so stopped making it. If you have a question regarding this software please ask

  • @silvereyes000
    @silvereyes000 3 місяці тому

    SRR390728

  • @MOIST_08
    @MOIST_08 3 місяці тому

    Bro how can i access files which are in pendrive, directly from terminal

  • @duafatima6283
    @duafatima6283 3 місяці тому

    Hi, Sir do you know how can we remove paralogs using bioinformatics?

  • @johirislam8174
    @johirislam8174 3 місяці тому

    Do you have whole video on WGS analysis from beginning to variant calling and annotation?

  • @abubakarraja7605
    @abubakarraja7605 3 місяці тому

    I have never understand it before. Thank you so much

  • @ShivangiMishra-wy4gj
    @ShivangiMishra-wy4gj 4 місяці тому

    I have installed pymol, filled the licence still it is not running on my windows. What is the step to do finally open pymol

  • @uksuperrascal
    @uksuperrascal 4 місяці тому

    Would be great if you used bigger terminal window and made terminal text bigger - Ctrl + Shift + + makes terminal text bigger.

  • @jameelabduljalil25
    @jameelabduljalil25 4 місяці тому

    May Allah accepted your hajj.

  • @gazwanasadi7437
    @gazwanasadi7437 4 місяці тому

    thank you sir I do really appreciatted

  • @andyelle8109
    @andyelle8109 4 місяці тому

    super helpful! thank you!

  • @adlanadlan1783
    @adlanadlan1783 4 місяці тому

    🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋🕋