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353 results • Page
1 of 8
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2
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Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 7 days ago by
ATpoint
70k • written 7 days ago by
Simon
▴ 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
Lars
▴ 970 • written 5.9 years ago by
jnowacki
▴ 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
Ram
38k • written 11 months ago by
dare_devil
★ 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
8 weeks ago by
barslmn
★ 1.4k
1
vote
1
reply
487
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 11 weeks ago by
Pierre Lindenbaum
153k • written 11 weeks ago by
barslmn
★ 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
28 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
Ram
38k • written 2.5 years ago by
ATpoint
70k
1
vote
3
replies
421
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbs
sampling
splice
updated 3 months ago by
GenoMax
127k • written 3 months 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
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 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
Ram
38k • written 5.6 years ago by
Kevin Blighe
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
Ram
38k • written 7.1 years ago by
Obi Griffith
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
Ram
38k • written 3.6 years ago by
Juke34
7.8k
1
vote
2
replies
547
views
Tutorial:
ViennaRNA package installation in Windows
install
mfold
viennarna
rna
windows
updated 6 months ago by
Asaf
9.6k • written 6 months ago by
Sandhiya
▴ 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 7 days ago by
krushnach80
★ 1.1k • written 4.4 years ago by
Kevin Blighe
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
Shubham
• 0 • written 2.1 years ago by
Novogene
▴ 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
Assa Yeroslaviz
★ 1.8k • written 14 months ago by
dariober
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
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
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
Vincent Laufer
★ 2.5k • written 8 months ago by
kodwings
▴ 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
Ram
38k • written 4.8 years ago by
egeulgen
★ 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
Ram
38k • written 9.8 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 20 days ago by
Ram
38k • written 5.3 years ago by
ahmad mousavi
▴ 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
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
3
votes
2
replies
1.4k
views
Tutorial:
Running fastq_screen on your data
fastqscreen
12 months ago by
rohitsatyam102
▴ 690
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
Angelina_G
• 0 • written 13 months ago by
thehung92phuyen
▴ 30
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 7 weeks ago by
Ram
38k • written 9.9 years ago by
Medhat
9.5k
25
votes
13
replies
6.8k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 14 months ago by
liorglic
★ 1.2k • written 17 months ago by
Istvan Albert
97k
3
votes
13
replies
9.4k
views
Tutorial:
Merging multiple vcf files into Single vcf file
merge
vcf
bcftools
updated 20 days ago by
Ram
38k • written 4.1 years ago by
jaybee
▴ 140
13
votes
9
replies
4.1k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 9 months ago by
dk0319
▴ 40 • written 16 months ago by
Barry Digby
★ 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
ATpoint
70k • written 15 months ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
7.9k
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
14 months ago by
Wayne
★ 1.7k
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
Ram
38k • written 2.1 years ago by
garden_giessen
▴ 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
Ram
38k • written 2.0 years ago by
Nitin Narwade
★ 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
41
votes
6
replies
18k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 14 months ago by
cameron.cowan
▴ 40 • written 2.0 years ago by
rpolicastro
11k
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
Ram
38k • written 5.4 years ago by
Kevin Blighe
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
brunobsouzaa
▴ 810 • written 18 months ago by
nhaus
▴ 280
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
6
votes
2
replies
1.0k
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
19 months ago by
Kevin Blighe
84k
0
votes
0
replies
897
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
19 months ago by
mo
• 0
2
votes
0
replies
1.8k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
20 months ago by
Kevin Blighe
84k
353 results • Page
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Recent Votes
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
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Answer: Any tips in landing a bioinformatic job?
by
Vincent Laufer
★ 2.5k
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…
Answer: Admixture cv error
by
Declan
• 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43
by
ahmad
• 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq
by
dsull
★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq
by
dsull
★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell
by
lethalfang
▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
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by
lethalfang
▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata?
by
jv
★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
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