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Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
1
vote
0
replies
2.3k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
5
votes
0
replies
1.2k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 5 months ago by 41k • written 11 months ago by ▴ 360
6
votes
0
replies
3.2k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
9 months ago by Novogene ▴ 360
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 9 months ago by 41k • written 3.2 years ago by 78k
1
vote
3
replies
788
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
8 months ago by barslmn ★ 2.0k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 9 months ago by 41k • written 6.2 years ago by 86k
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 8 months ago by 41k • written 4.3 years ago by 8.4k
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
1
vote
0
replies
705
views
Tutorial: Making LDA Score plot
LDA metagenomics
14 months ago by rohitsatyam102 ▴ 780
132
votes
123
replies
34k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.7 years ago by ▴ 360
15
votes
1
reply
3.4k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 15 months ago by ★ 1.8k • written 23 months ago by 14k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
27
votes
0
replies
3.4k
views
Tutorial: Building Docker images
singularity docker container
16 months ago by ATpoint 78k
2
votes
1
reply
49k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 16 months ago by 3.8k • written 16 months ago by ▴ 20
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 8 months ago by 41k • written 6.0 years ago by ▴ 770
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
3
votes
2
replies
2.4k
views
Tutorial: Running fastq_screen on your data
fastqscreen
20 months ago by rohitsatyam102 ▴ 780
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 years ago by 99k
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
16
votes
9
replies
6.2k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 17 months ago by ▴ 70 • written 24 months ago by ★ 1.3k
0
votes
0
replies
11k
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
23 months ago by Wayne ★ 1.8k
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 9 months ago by 41k • written 2.8 years ago by ▴ 130
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 8 months ago by 41k • written 2.7 years ago by ★ 1.5k
44
votes
6
replies
22k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
15
votes
2
replies
1.9k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 13 months ago by ▴ 820 • written 2.2 years ago by ▴ 280
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 months ago by 41k • written 11.2 years ago by 20k
6
votes
2
replies
1.5k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.3 years ago by Kevin Blighe 86k
0
votes
0
replies
1.1k
views
Tutorial: Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge kallisto rnaseq sleuth
2.3 years ago by mo • 0
2
votes
0
replies
2.8k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
2.3 years ago by Kevin Blighe 86k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.3 years ago by 86k
0
votes
0
replies
1.0k
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
2.5 years ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
1.2k
views
Tutorial: Slurm and parallelization
slurm
2.5 years ago by Juke34 8.4k
1
vote
0
replies
1.2k
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
2.5 years ago by Pratik ▴ 940
13
votes
1
reply
2.7k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 2.5 years ago by ★ 16k • written 2.5 years ago by 86k
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
4
votes
0
replies
1.1k
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
2.5 years ago by pbpanigrahi ▴ 420
0
votes
1
reply
985
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.5 years ago by 21k • written 2.5 years ago by ★ 1.1k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
4
votes
2
replies
2.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
51
votes
14
replies
79k
views
10 follow
Tutorial: Using R in Conda
R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 780
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
383 results • Page 2 of 8
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Comment: Tools or R / Python packages to perfom ML models
Comment: Tools or R / Python packages to perfom ML models
Comment: p-value combination methods
Answer: bcftools mpileup --max depth : What would be a reasonable setting for this optio
Answer: bcftools mpileup --max depth : What would be a reasonable setting for this optio
Answer: What type of cancer did they study in this paper?
Answer: How to filter .fasta file based on conditional statement
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Comment: Tools or R / Python packages to perfom ML models by Matthias Zepper 4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
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> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
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My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by rpolicastro 12k
They could have saved themselves a ton of money by sequencing this on a miseq.
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I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
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It's not stupid, just a bit lazy ;-)
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Hi, did you find an effective solution for this problem? beside Agat and
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Thank you. I asked a stupid question.
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First hit on google: https://stackoverflow.com/questions/73935357/error-in-grid-callc-convert-x-as-integerwhatfrom-as-integerwhatto-vie
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Hi, Scaling all features might be useful to plot genes that are not among the 2k HVG in a heatmap. Otherwise than that, I never encounter…
Comment: How to filter .fasta file based on conditional statement by rob_DNA ▴ 20
Oh wow that was a bit stupid.. I downloaded 39.06 but I accidentally used 39.01... anyway, thank you very much for your help!! I now used t…
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Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
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A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
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