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356 results • Page
1 of 8
Sort: Rank
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Votes
Replies
3
votes
0
replies
319
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
GenoMax
129k • written 9.5 years ago by
Obi Griffith
20k
2
votes
0
replies
450
views
Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 10 weeks ago by
ATpoint
72k • written 10 weeks ago by
Simon
▴ 40
1
vote
0
replies
277
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 23 days ago by
Ram
39k • written 6.1 years ago by
jnowacki
▴ 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
Randy H
▴ 100 • written 9 months ago by
Kevin Blighe
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
Ram
39k • written 13 months ago by
dare_devil
★ 3.1k
1
vote
0
replies
470
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
769
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 4 months ago by
Pierre Lindenbaum
154k • written 4 months ago by
barslmn
★ 1.6k
1
vote
0
replies
717
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
611
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
737
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
559
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
Ram
39k • written 2.7 years ago by
ATpoint
72k
1
vote
3
replies
512
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
cmdcolin
★ 3.0k • written 4.9 years ago by
otwtgin2010
▴ 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
Ram
39k • written 5.7 years ago by
Kevin Blighe
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
Ram
39k • written 7.2 years ago by
Obi Griffith
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
Ram
39k • written 3.8 years ago by
Juke34
7.9k
1
vote
2
replies
740
views
Tutorial:
ViennaRNA package installation in Windows
install
mfold
viennarna
rna
windows
updated 8 months ago by
Asaf
9.6k • written 8 months ago by
Sandhiya
▴ 20
1
vote
0
replies
403
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
1769mkc
★ 1.1k • written 4.6 years ago by
Kevin Blighe
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 16 days ago by
Ram
39k • written 2.3 years ago by
Novogene
▴ 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
Assa Yeroslaviz
★ 1.8k • written 17 months ago by
dariober
14k
14
votes
9
replies
4.2k
views
6 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
aspera
ascp
updated 4 weeks ago by
sjlee4019
• 0 • written 11 months ago by
ATpoint
72k
83
votes
21
replies
16k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 weeks ago by
Ram
39k • written 2.6 years ago by
Hamid Ghaedi
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
Vincent Laufer
★ 2.9k • written 10 months ago by
kodwings
▴ 10
83
votes
34
replies
16k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 8 days ago by
adelheidkratzer
• 0 • written 5.0 years ago by
egeulgen
★ 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
Ram
39k • written 9.9 years ago by
Eric Normandeau
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
Ram
39k • written 5.5 years ago by
ahmad mousavi
▴ 750
38
votes
8
replies
10k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 12 weeks ago by
Ram
39k • written 2.7 years ago by
Hamid Ghaedi
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
Angelina_G
• 0 • written 15 months ago by
thehung92phuyen
▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 3 months ago by
Ram
39k • written 10.0 years ago by
Medhat
9.6k
27
votes
13
replies
8.2k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 16 months ago by
liorglic
★ 1.2k • written 19 months ago by
Istvan Albert
98k
3
votes
13
replies
10k
views
Tutorial:
Merging multiple vcf files into Single vcf file
merge
vcf
bcftools
updated 12 weeks ago by
Ram
39k • written 4.3 years ago by
jaybee
▴ 140
16
votes
9
replies
4.6k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 11 months ago by
dk0319
▴ 70 • written 18 months ago by
Barry Digby
★ 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 4 days ago by
Ram
39k • written 17 months ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
9.3k
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
Ram
39k • written 2.3 years ago by
garden_giessen
▴ 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
Ram
39k • written 2.2 years ago by
Nitin Narwade
★ 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
cameron.cowan
▴ 40 • written 2.2 years ago by
rpolicastro
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
k001
▴ 10 • written 5.5 years ago by
Kevin Blighe
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
brunobsouzaa
▴ 810 • written 20 months ago by
nhaus
▴ 280
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
6
votes
2
replies
1.1k
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
21 months ago by
Kevin Blighe
85k
356 results • Page
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Recent Votes
How to make the profile line of `deepTools::plotHeatmap` more smooth?
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
Comment: Getting species names and taxa id from assembly accession number
Comment: STAR GenomeIndex output (which is the BAM file?)
Answer: [Meta] Use of AI
Answer: h5ad cellxgene to R
Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
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Recent Replies
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kevin Blighe
85k
Hello friend. Life moves on...
Comment: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Dan
▴ 120
Do you mean I should check the intersections between the peaks in the `bed` file using `bedtools intersect` (https://bedtools.readthedocs.i…
Answer: How to make the profile line of `deepTools::plotHeatmap` more smooth?
by
Trivas
★ 1.2k
Your issue is with your bed file then, not necessarily with deep tools. I'd look into the bedtools suite to see if you can minimize overlap…
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
https://www.biostars.org/p/492331/
Comment: variant allelic fraction
by
malm
• 0
ok how can i calculate it from the vep file?
Comment: Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads
by
benformatics
3.6k
I think it would be fair (and conservative) to remove read pairs where one maps to the mitochondrial genome. It should be a relatively very…
Answer: Convert Bam file to Fastq
by
Michael
52k
I think your code is incorrect bash syntax. I think you want something like this: sort bam_headers.txt > bam_haeders-sorted.txt # c…
Comment: Combination of ROC CURVE
by
Maria17
▴ 20
For example, if three targets are combined and the mean value is plotted, the different combinations give different numbers, but there are …
Comment: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
by
Kermit
▴ 80
neither simple nor helpful, but perhaps the OP changed his question away from "why might diff models produce diff results" to the current "…
Comment: Convert Bam file to Fastq
by
Michael
52k
At first, I would trust samtools to do the right thing but of course it doesn't hurt to double check. But I think the crux is what is in fa…
Comment: Convert Bam file to Fastq
by
Pierre Lindenbaum
154k
paste fastq1_read_ids.txt fastq2_read_ids.txt is a tabular file with two column. Is it the same for bam_read_names.txt ?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
this is not a field provided by VEP.
Answer: WGCNA Trait File Issues
by
Jennifer M
• 0
![enter image description here][1] [1]: /media/images/0cf4eaa7-9550-4bbb-b43e-208dc787
Comment: Pairwise Alignment
by
WouterDeCoster
47k
> for whole genome analysis What do you mean with that? You provide too little information for us to answer your question.
Comment: Getting species names and taxa id from assembly accession number
by
GenoMax
129k
There must be some temporary glitch. Following command works (via EntrezDirect): $ esearch -db assembly -query GCA_000001405.29 | esu…
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