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323 results • Page 1 of 7
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3
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0
replies
310
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Tutorial: How to make a heatmap in R and deep understand it
heatmap r
29 days 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 29 days ago by 129k • written 9.5 years ago by 20k
2
votes
0
replies
448
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 10 weeks ago by 72k • written 10 weeks ago by ▴ 40
1
vote
0
replies
275
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 21 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 7 weeks ago by ▴ 100 • written 9 months ago by 85k
3
votes
3
replies
1.6k
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 13 months ago by ★ 3.1k
1
vote
0
replies
466
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
1.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
9 weeks ago by barslmn ★ 1.6k
1
vote
1
reply
763
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
714
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
4 months ago by Dr.Animo ▴ 50
1
vote
0
replies
607
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
734
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
557
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
509
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 12 weeks ago by 39k • written 3.8 years ago by 7.9k
1
vote
2
replies
732
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
402
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 10 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 14 days ago by 39k • written 2.2 years ago by ▴ 300
12
votes
1
reply
2.6k
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
4.2k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 29 days 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 12 weeks 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 7 days ago by • 0 • written 4.9 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 12 weeks 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 12 weeks ago by 39k • written 2.7 years ago by 2.9k
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 10.0 years ago by 9.6k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 12 weeks ago by 39k • written 4.3 years ago by ▴ 140
16
votes
9
replies
4.6k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 11 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 2 days ago by 39k • written 17 months ago by ▴ 20
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 12 weeks 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
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 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
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 11 weeks ago by 39k • written 4.8 years ago by 85k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 11 weeks ago by 39k • written 4.9 years ago by 72k
65
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 11 weeks ago by 39k • written 4.2 years ago by 16k
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 14k
323 results • Page 1 of 7
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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