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Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
1 day ago by Coremine Medical ▴ 10
1
vote
0
replies
121
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 2 days ago by 39k • written 2 days ago by ▴ 10
3
votes
0
replies
333
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
4 weeks ago by Ming Tommy Tang ★ 2.9k
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 weeks ago by 130k • written 9.5 years ago by 20k
2
votes
0
replies
467
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 11 weeks ago by 72k • written 11 weeks ago by ▴ 40
1
vote
0
replies
288
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
11 weeks ago by Milad ▴ 10
3
votes
2
replies
2.1k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 26 days ago by 39k • written 6.1 years ago by ▴ 100
7
votes
3
replies
1.2k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 8 weeks ago by ▴ 100 • written 10 months ago by 85k
3
votes
3
replies
1.7k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 3 months ago by 39k • written 14 months ago by ★ 3.1k
1
vote
0
replies
477
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
4 months ago by firestar ★ 1.5k
10
votes
7
replies
1.4k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
9 weeks ago by barslmn ★ 1.6k
1
vote
1
reply
789
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 4 months ago by 154k • written 4 months ago by ★ 1.6k
1
vote
0
replies
731
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
5 months ago by Dr.Animo ▴ 50
1
vote
0
replies
622
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
5 months ago by Novogene ▴ 300
1
vote
0
replies
746
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo mining differential data expression RNA-Seq gene R
5 months ago by Novogene ▴ 300
2
votes
0
replies
565
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
5 months ago by Novogene ▴ 300
4
votes
0
replies
1.3k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
3 months ago by Novogene ▴ 300
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
1
vote
3
replies
518
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
9 weeks ago by barslmn ★ 1.6k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 3 months ago by 39k • written 3.8 years ago by 7.9k
1
vote
2
replies
756
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 8 months ago by 9.6k • written 8 months ago by ▴ 20
1
vote
0
replies
406
views
Tutorial: Making LDA Score plot
LDA metagenomics
8 months ago by rohitsatyam102 ▴ 690
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 11 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
11
votes
7
replies
7.4k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 19 days ago by 39k • written 2.3 years ago by ▴ 300
12
votes
1
reply
2.7k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 9 months ago by ★ 1.8k • written 17 months ago by 14k
14
votes
9
replies
4.3k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 4 weeks ago by • 0 • written 11 months ago by 72k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 3 months ago by 39k • written 2.6 years ago by 2.9k
27
votes
0
replies
2.9k
views
Tutorial: Building Docker images
singularity docker container
10 months ago by ATpoint 72k
1
vote
1
reply
27k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 10 months ago by ★ 2.9k • written 10 months ago by ▴ 10
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 days ago by • 0 • written 5.0 years ago by ★ 1.3k
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 3 months ago by 39k • written 5.5 years ago by ▴ 750
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 3 months ago by 39k • written 2.7 years ago by 2.9k
3
votes
2
replies
1.6k
views
Tutorial: Running fastq_screen on your data
fastqscreen
14 months ago by rohitsatyam102 ▴ 690
7
votes
14
replies
2.4k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 7 months ago by • 0 • written 15 months ago by ▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.1 years ago by 9.6k
27
votes
13
replies
8.3k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 16 months ago by ★ 1.2k • written 20 months ago by 98k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 3 months ago by 39k • written 4.3 years ago by ▴ 140
16
votes
9
replies
4.7k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 12 months ago by ▴ 70 • written 18 months ago by ★ 1.1k
2
votes
0
replies
1.2k
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
updated 7 days ago by 39k • written 17 months ago by ▴ 20
0
votes
0
replies
9.4k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
17 months ago by Wayne ★ 1.8k
12
votes
4
replies
4.7k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 3 months ago by 39k • written 2.3 years ago by ▴ 120
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 3 months ago by 39k • written 2.2 years ago by ★ 1.3k
6
votes
2
replies
2.9k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
8 months ago by Hamid Ghaedi 2.9k
42
votes
6
replies
19k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 16 months ago by ▴ 40 • written 2.2 years ago by 12k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
15
votes
2
replies
1.6k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 7 months ago by ▴ 810 • written 20 months ago by ▴ 280
358 results • Page 1 of 8
Recent Votes
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
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Recent Replies
Comment: Creating a local version of Clustered NR database by GenoMax 130k
> One idea is to provide just the representative sequences as a first > pass. This seems reasonable since it should capture significant pa…
Comment: pal2nal -nogap -nomismatch options not working by Marie • 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq? by rpolicastro 12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq? by Trivas ★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap? by Ram 39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag by Ram 39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database by PeterC_NCBI ▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R by rohitsatyam102 ▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38 by GenoMax 130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag by Pierre Lindenbaum 154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Ram 39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag by Ram 39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38 by heureuse • 0
Thank you very much. I get it from UCSC.
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