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412 results • Page
2 of 9
Sort: Rank
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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
548
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
651
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
682
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
748
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
686
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 14 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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Answer: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
A: Insert Size And Fragment Size ?
Answer: samtools 1.0 'index' : CSI index vs BAI index ?
Comment: Nextflow and self-made pipelines opinion
Comment: Nextflow and self-made pipelines opinion
What is Deepvariant default filtering values ?
Answer: Nextflow: how to get the process work dir, within the process
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I've done what I can to make your post more professional. Stick to outlining your problem, personal pleas do not really belong on a profess…
Comment: Contig assembly task, errors
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Hi Phillip, Thanks for providing an answer and clearing up some confusion, looking into what you said about older assemblers reverse comp…
Comment: How to analyze Infinium Mouse Methylation BeadChip array data?
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Did you get this figured out? I am having the same error in R.
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Try this: ```r #Read the motifs library(JASPAR2024) library(TFBSTools) jaspar <- JASPAR2024() sq24 <- RSQLite::dbConnect(RSQLite::SQLite…
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It's not possible. Gene counts are a region aggregate, bigwigs are a per-base readout and you cannot use normalized counts for mentioned to…
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Thank you Pierre! Not sure why I didn't notice that (I should have)
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bigwig is chrom/start/end/value . what kind of matrix do you want ?
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I want to use the matrix derived from bigwig files to perform different analysis by DESeq2 or edgeR.
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I have uploaded the ExomeCNV (v1.4) user manual [here][1]. [1]: https://fastupload.io/hZbU
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I assume you mean "server" as in local hardware that you own/control since "cloud" is a just bunch of servers on internet that you rent (pa…
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I think that is more a matter of convenience and legality. It mostly depends on who pays for it and what you prefer. Both solutions should …
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> could you please explain what the collate does? http://www.htslib.org/doc/samtools-collate.html
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Same keeps happening to me; but it is weird, I corrected the batch effect with the same exact function a few months ago and worked fine. I …
Comment: How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when ru
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Thank you for the feedback! I already used just the `samtools fastq -1 R1.fq.gz -2 R2.fq.gz -s Rx.fq.gz -0 R0.fq.gz`. Could you please exp…
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