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408 results • Page 2 of 9
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7
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0
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585
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Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
1
vote
0
replies
625
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 8 months ago by 43k • written 8 months ago by ★ 3.9k
3
votes
1
reply
632
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 8 months ago by 43k • written 8 months ago by 8.5k
84
votes
29
replies
32k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 8 months ago by • 0 • written 8.1 years ago by 20k
1
vote
0
replies
674
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
21
votes
13
replies
10k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 months ago by • 0 • written 21 months ago by 81k
2
votes
0
replies
3.1k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
19
votes
7
replies
6.5k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 9 months ago by 81k • written 4.1 years ago by 6.3k
4
votes
2
replies
1.0k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 months ago by Ming Tommy Tang ★ 3.9k
93
votes
23
replies
91k
views
15 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 12 weeks ago by • 0 • written 5.7 years ago by ▴ 610
2
votes
0
replies
464
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
4
votes
0
replies
757
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
9 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
646
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
0
votes
0
replies
644
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
9 months ago by sinha.shriprakash ▴ 20
1
vote
2
replies
865
views
Tutorial: How to ask computational biology questions
computational-biology
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
0
replies
676
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
2
votes
0
replies
713
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
10 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
600
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
659
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
10 months ago by Coremine Medical ▴ 20
2
votes
0
replies
698
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 10 months ago by 43k • written 10 months ago by ▴ 20
4
votes
0
replies
944
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
11 months ago by Ming Tommy Tang ★ 3.9k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 11 months ago by 141k • written 10.4 years ago by 20k
2
votes
0
replies
994
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 13 months ago by 81k • written 13 months ago by ▴ 40
1
vote
0
replies
808
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 5 months ago by 43k • written 13 months ago by ▴ 10
3
votes
2
replies
2.6k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
7
votes
3
replies
2.5k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 12 months ago by ▴ 110 • written 20 months ago by 87k
3
votes
3
replies
2.8k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 14 months ago by 43k • written 2.0 years ago by ★ 4.3k
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 5 months ago by • 0 • written 14 months ago by ★ 1.6k
11
votes
7
replies
2.2k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
12 months ago by barslmn ★ 2.1k
2
votes
1
reply
2.6k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 15 months ago by 161k • written 15 months ago by ★ 2.1k
7
votes
2
replies
2.5k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
9 months ago by Dr.Animo ▴ 130
2
votes
0
replies
1.2k
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 10 months ago by 43k • written 15 months ago by ▴ 410
1
vote
0
replies
2.6k
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 10 months ago by 43k • written 15 months ago by ▴ 410
5
votes
0
replies
1.6k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 10 months ago by 43k • written 15 months ago by ▴ 410
6
votes
0
replies
5.2k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
13 months ago by Novogene ▴ 410
49
votes
1
reply
8.7k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 14 months ago by 43k • written 3.6 years ago by 81k
1
vote
3
replies
946
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
12 months ago by barslmn ★ 2.1k
73
votes
60
replies
27k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 14 months ago by 43k • written 6.6 years ago by 87k
14
votes
31
replies
6.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 13 months ago by 43k • written 4.7 years ago by 8.5k
1
vote
2
replies
1.5k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 20
1
vote
0
replies
909
views
Tutorial: Making LDA Score plot
LDA metagenomics
19 months ago by rohitsatyam102 ▴ 840
133
votes
123
replies
38k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 13 months ago by ★ 1.2k • written 5.5 years ago by 87k
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.1 years ago by ▴ 410
15
votes
1
reply
3.9k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 19 months ago by ★ 1.8k • written 2.3 years ago by 14k
28
votes
0
replies
3.6k
views
Tutorial: Building Docker images
singularity docker container
21 months ago by ATpoint 81k
2
votes
1
reply
59k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 21 months ago by 4.2k • written 21 months ago by ▴ 20
83
votes
34
replies
18k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 10 months ago by • 0 • written 5.8 years ago by ★ 1.3k
87
votes
2
replies
59k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 13 months ago by 43k • written 10.8 years ago by 11k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 13 months ago by 43k • written 6.4 years ago by ▴ 800
3
votes
2
replies
2.8k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.1 years ago by rohitsatyam102 ▴ 840
408 results • Page 2 of 9
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Can I liftover hs37d5 to hg38 using hg19ToHg38 chain file?
Comment: Removing duplicates
Comment: Removing duplicates
High fold change values
C: Bcftools Mpileup Removes Marked Duplicates?
Prediction tools summary - zero values
A: Error with Formatdb of legacy blast?
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Recent Replies
Comment: Removing duplicates by quentinperriere • 0
thank you for responding. I was looking for suitable variant calling tool. I'm working on fungus and I don't have fast5 files. Could you re…
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. I see S-mode in the CIBERSORTx official website tutorial(https://cibersortx.stanford.edu/), and the imag…
Comment: How to reduce the variation of CIBERSORTx results? by LChart 3.9k
First time I've heard of S-mode. I imagine you've seen this benchmark where it doesn't come out too well: https://academic.oup.com/bib/arti…
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084521725806
Comment: ISCN annotation for SV/CN VCF files by adedare • 0
https://res.saletool.cn/vcf/18084435127462
Comment: How can I solve this error? by 22211020193 • 0
I want to conduct GWAS meta-analysis using metal software.
Comment: How to reduce the variation of CIBERSORTx results? by feather-W • 0
Hi LChart, Thanks for your reply. Yes, the identical command lines produce different results in CIBERSORTx S-mode. Although I input the da…
Comment: Removing duplicates by joe ▴ 500
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates by samuel.a.odonnell ▴ 520
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis by geneontologyhelp ▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data? by etiennedanis ▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates by joe ▴ 500
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together? by GenoMax 141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions by swbarnes2 14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates by quentinperriere • 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
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