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231 results • Page 1 of 5
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Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 7 days ago by 70k • written 7 days ago by ▴ 30
1
vote
0
replies
126
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
13 days ago by Milad ▴ 10
3
votes
2
replies
2.0k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
blogs Workshops conferences tutorials
updated 4 weeks ago by ▴ 970 • written 5.9 years ago by ▴ 100
5
votes
2
replies
813
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
5 weeks ago by Kevin Blighe 84k
1
vote
3
replies
1.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 6 weeks ago by 38k • written 11 months ago by ★ 1.7k
1
vote
0
replies
341
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
9 weeks ago by firestar ★ 1.5k
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
2 hours ago by barslmn ★ 1.4k
1
vote
1
reply
489
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 11 weeks ago by 153k • written 11 weeks ago by ★ 1.4k
1
vote
0
replies
425
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
rRNA RNAmmer Annotation Genome
12 weeks ago by Dr.Animo ▴ 50
0
votes
0
replies
461
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo mining enrichment data Gene pathway RNA-Seq R
3 months ago by Novogene ▴ 240
1
vote
0
replies
552
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
12 weeks ago by Novogene ▴ 240
1
vote
0
replies
375
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo mining datasets data SRA RNA-Seq
3 months ago by Novogene ▴ 240
2
votes
0
replies
645
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
29 days ago by Novogene ▴ 240
44
votes
1
reply
6.2k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 6 weeks ago by 38k • written 2.5 years ago by 70k
1
vote
3
replies
423
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
2 hours ago by barslmn ★ 1.4k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 years ago by 20k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 20 days ago by 38k • written 3.6 years ago by 7.8k
1
vote
2
replies
547
views
Tutorial: ViennaRNA package installation in Windows
install mfold viennarna rna windows
updated 6 months ago by 9.6k • written 6 months ago by ▴ 20
1
vote
0
replies
315
views
Tutorial: Making LDA Score plot
LDA metagenomics
6 months ago by rohitsatyam102 ▴ 690
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 days ago by ★ 1.1k • written 4.4 years ago by 84k
9
votes
7
replies
6.1k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 240
11
votes
1
reply
2.3k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 6 months ago by ★ 1.8k • written 14 months ago by 14k
13
votes
8
replies
3.2k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
4 months ago by ATpoint 70k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
27
votes
0
replies
2.7k
views
Tutorial: Building Docker images
singularity docker container
8 months ago by ATpoint 70k
1
vote
1
reply
19k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 8 months ago by ★ 2.6k • written 8 months ago by ▴ 10
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 20 days ago by 38k • written 4.8 years ago by ★ 1.3k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 4 weeks ago by 38k • written 9.8 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 20 days ago by 38k • written 5.3 years ago by ▴ 740
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
7
votes
14
replies
2.1k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 months ago by • 0 • written 13 months ago by ▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 weeks ago by 38k • written 9.9 years ago by 9.5k
3
votes
13
replies
9.5k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 20 days ago by 38k • written 4.1 years ago by ▴ 140
13
votes
9
replies
4.1k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 16 months ago by ★ 1.1k
2
votes
0
replies
1.1k
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell Biology R Computational signalling
updated 7 weeks ago by 70k • written 15 months ago by ▴ 20
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 weeks ago by 38k • written 2.1 years ago by ▴ 120
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 20 days ago by 38k • written 2.0 years ago by ★ 1.3k
6
votes
2
replies
2.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene RNA-seq expression clustering
6 months ago by Hamid Ghaedi 2.9k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 16 days ago by 38k • written 5.4 years ago by 84k
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 280
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 weeks ago by 38k • written 10.5 years ago by 20k
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 16 days ago by 38k • written 4.6 years ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 16 days ago by 38k • written 4.7 years ago by 70k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 15 days ago by 38k • written 3.8 years ago by ★ 14k
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 690
231 results • Page 1 of 5
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Easy way to run easily orthoMCL (Copy & paste)
Answer: Any tips in landing a bioinformatic job?
Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: Any tips in landing a bioinformatic job?
Answer: What is the NCBI's definition of an "atypical genome"?
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Answer: Extract data from Signac RegionMatrix? by Chironex ▴ 40
object@assays$ATAC@positionEnrichment$my_region_matrix and also object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job? by ATpoint 70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets by ATpoint 70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
Comment: using CITE-seq data to cluster single cells by ATpoint 70k
If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
Answer: Align miRNA library (small RNA-seq) without trimming by ATpoint 70k
For miRNA you should trim the data to the actual expected miRNA length (20-something bp, I would need to look up the exact value). Reason i…
Comment: boxplot issue by ATpoint 70k
Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
Answer: Total No of Genes of GENCODE Release 43 by ATpoint 70k
As I said, I assume that you are doing something on old/overwritten variables or a wrong GTF. This is how it is: a<-rtracklayer::i…
Answer: Any tips in landing a bioinformatic job? by Vincent Laufer ★ 2.6k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming by Paola ▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming by Ming Tommy Tang ★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression by afei • 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa by rebeliscu ▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an by cfos4698 ▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking by Mensur Dlakic ★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
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