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412 results • Page
2 of 9
Sort: Rank
Rank
Views
Votes
Replies
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
0
votes
0
replies
687
views
Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
8 months ago by
Ming Tommy Tang
★ 3.9k
14
votes
3
replies
20k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 8 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
8
votes
2
replies
1.1k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 8 months ago by
Ram
43k • written 8 months ago by
carlopecoraro2
★ 2.5k
1
vote
0
replies
547
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
8 months ago by
Ming Tommy Tang
★ 3.9k
10
votes
4
replies
5.6k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
9 months ago by
Hamid Ghaedi
3.2k
7
votes
0
replies
602
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
1
vote
0
replies
642
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
1
reply
650
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 9 months ago by
Ram
43k • written 9 months ago by
Juke34
8.6k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.2 years ago by
Obi Griffith
20k
1
vote
0
replies
692
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
21
votes
13
replies
10k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 6 months ago by
jude
• 0 • written 22 months ago by
ATpoint
82k
2
votes
0
replies
3.2k
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 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
19
votes
7
replies
6.6k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 9 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
4
votes
2
replies
1.1k
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
92k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
2
votes
0
replies
482
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
783
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
681
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
661
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
10 months ago by
sinha.shriprakash
▴ 20
1
vote
2
replies
890
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
693
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 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
747
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
615
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
685
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
11 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
724
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 11 months ago by
Ram
43k • written 11 months ago by
Coremine Medical
▴ 20
4
votes
0
replies
962
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
12 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 12 months ago by
GenoMax
142k • written 10.5 years ago by
Obi Griffith
20k
2
votes
0
replies
1.0k
views
Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 13 months ago by
ATpoint
82k • written 13 months ago by
Simon
▴ 40
1
vote
0
replies
828
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 6 months ago by
Ram
43k • written 13 months ago by
Milad
▴ 10
3
votes
2
replies
2.7k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 12 months ago by
Ram
43k • written 7.0 years ago by
jnowacki
▴ 100
7
votes
3
replies
2.6k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 13 months ago by
Randy H
▴ 110 • written 21 months ago by
Kevin Blighe
87k
3
votes
3
replies
2.9k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC
TCGABiolinks
STAR
updated 14 months ago by
Ram
43k • written 2.1 years ago by
DareDevil
★ 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
Ali
• 0 • written 15 months ago by
firestar
★ 1.6k
11
votes
7
replies
2.3k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
13 months ago by
barslmn
★ 2.1k
2
votes
1
reply
2.7k
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 16 months ago by
Pierre Lindenbaum
161k • written 16 months ago by
barslmn
★ 2.1k
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
Ram
43k • written 16 months ago by
Novogene
▴ 420
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
Ram
43k • written 16 months ago by
Novogene
▴ 420
5
votes
0
replies
1.7k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
6
votes
0
replies
5.5k
views
Tutorial:
How to download GEO data Quickly and easily
geo
RNA-Seq
R
data-mining
14 months ago by
Novogene
▴ 420
50
votes
1
reply
8.8k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 15 months ago by
Ram
43k • written 3.7 years ago by
ATpoint
82k
1
vote
3
replies
964
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbssampling
splice
13 months ago by
barslmn
★ 2.1k
73
votes
60
replies
28k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 15 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
87k
14
votes
31
replies
6.8k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 14 months ago by
Ram
43k • written 4.7 years ago by
Juke34
8.6k
1
vote
2
replies
1.6k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 10 months ago by
Ram
43k • written 19 months ago by
Sandhiya
▴ 20
1
vote
0
replies
935
views
Tutorial:
Making LDA Score plot
LDA
metagenomics
19 months ago by
rohitsatyam102
▴ 850
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
1769mkc
★ 1.2k • written 5.6 years ago by
Kevin Blighe
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
Ram
43k • written 3.2 years ago by
Novogene
▴ 420
15
votes
1
reply
4.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 20 months ago by
Assa Yeroslaviz
★ 1.8k • written 2.3 years ago by
dariober
14k
28
votes
0
replies
3.7k
views
Tutorial:
Building Docker images
singularity
docker
container
21 months ago by
ATpoint
82k
412 results • Page
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Recent Votes
A: How to get SNP identifiers from VCF file?
Answer: How can I analyze normalized expression data?
Answer: How can I analyze normalized expression data?
Answer: Pruning Phylogenetic Trees and Bootstrap Values
Difference between Pysam Pileup and Fetch
Answer: Where can I download some example BAM files?
Comment: Where can I download some example BAM files?
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Recent Replies
Answer: Seurat CellCycleScoring – confused about the proper order of operations when usi
by
Li
• 0
I‘m not an expert in sctransform or cellcyclescoring. But I think it's because sctransform creates a new assay named "SCT", which is differ…
Comment: How can I analyze normalized expression data?
by
mnx0723
• 0
thank you for comment
Comment: Pruning Phylogenetic Trees and Bootstrap Values
by
Zeng Hao
▴ 40
Dear Klaus, Thank you for the reply. If I could clarify with an example: With this tree, B0----------------- A -| B1----------…
Answer: Contig assembly task, errors
by
Philipp Bayer
8.4k
Feels a bit strange for an aptitude test, feels more like homework. 1) seems OK to me, just chuck them into CAP3 and see what falls out.…
Comment: Help with Biopython for Beginner
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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Answer: bcftools - reducing to "sites-only"?
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161k
bcftools view -G in.vcf.gz <!-- Diabetic foot ulceration (DFU) is a devastating complication of diabetes whose pathogenesis rema…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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• 0
I probably got some of the vocabulary wrong. I thought that "Dom HOR2932 HOR3036 HOR3726 KWSBambina Rec S42IL_124" were representing my ge…
Comment: featureCounts output assigned value higher than and HISAT2 mapping.
by
Ram
43k
It's featureCount**s**, not featureCount. I've edited your post and fixed all mentions of featureCounts.
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by
Emanoelle
• 0
Hey, I know it's been 5 years but I have the same issue. When I run the test the software is unable to perform and always deliver the follo…
Comment: STAR aligner error
by
Ram
43k
If they can't help you, we probably can't do much either. But we can optimize your STAR command. BAM SortedByCoordinate is the worst settin…
Answer: Obtaining Infinium Methylation450K manifest for hg38
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marco.barr
▴ 90
Hi, you can check it from github here: [https://zwdzwd.github.io/InfiniumAnnotation][1]. I don't know if this is what you are looking fo…
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ATpoint
82k
It makes absolutely no sense to conduct such an analysis. I strongly discourage you to even start with it. Results will be utterly nonsense…
Comment: Differentail gene expression results
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swbarnes2
14k
Cross-posted: https://support.bioconductor.org/p/9158194/
Answer: Seurat V5 integration
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5.3k
It will depend on your context and question. I guess you will want to compare gene expression between your conditions within cell types …
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by
Adam
▴ 30
You get this error when you try to compare two data frames that have different dimensions. Try using the traceback() command to figure out …
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