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383 results • Page
1 of 8
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0
votes
0
replies
167
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
4 days ago by
rohitsatyam102
▴ 780
36
votes
14
replies
32k
views
14 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 23 days ago by
psschlogl
▴ 50 • written 3.3 years ago by
lavinia.gordon
▴ 160
0
votes
0
replies
239
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
25 days ago by
rohitsatyam102
▴ 780
0
votes
4
replies
440
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
19 days ago by
Coremine Medical
▴ 20
90
votes
48
replies
31k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 27 days ago by
Ram
41k • written 10.1 years ago by
Irsan
★ 7.8k
48
votes
30
replies
9.3k
views
11 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
ATpoint
78k • written 7.7 years ago by
Ram
41k
1
vote
0
replies
264
views
Tutorial:
How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq
heatmap
rstats
TCGA
4 weeks ago by
Ming Tommy Tang
★ 3.6k
10
votes
31
replies
9.9k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 weeks ago by
ha2606
• 0 • written 5.9 years ago by
vimalkvn
▴ 320
2
votes
0
replies
363
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 10 weeks ago by
Ram
41k • written 10 weeks ago by
Pierre Lindenbaum
158k
0
votes
1
reply
314
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 11 weeks ago by
ATpoint
78k • written 11 weeks ago by
JC
▴ 30
4
votes
2
replies
2.5k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 12 weeks ago by
GenoMax
136k • written 3.6 years ago by
ATpoint
78k
0
votes
0
replies
421
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
3 months ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
365
views
Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
3 months ago by
Ming Tommy Tang
★ 3.6k
13
votes
3
replies
14k
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 3 months ago by
William
▴ 20 • written 6.7 years ago by
kirannbishwa01
★ 1.6k
5
votes
2
replies
685
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 3 months ago by
Ram
41k • written 3 months ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
315
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
3 months ago by
Ming Tommy Tang
★ 3.6k
9
votes
4
replies
4.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
3 months ago by
Hamid Ghaedi
3.1k
6
votes
0
replies
355
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
3 months ago by
barslmn
★ 2.0k
0
votes
0
replies
498
views
Tutorial:
How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq
seurat
scanpy
Python
3 months ago by
Starlitnightly
• 0
1
vote
0
replies
421
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 4 months ago by
Ram
41k • written 4 months ago by
Ming Tommy Tang
★ 3.6k
3
votes
1
reply
435
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 4 months ago by
Ram
41k • written 4 months ago by
Juke34
8.4k
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 4 months ago by
amziepickles
• 0 • written 7.7 years ago by
Obi Griffith
20k
1
vote
0
replies
468
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 4 months ago by
Ram
41k • written 4 months ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
643
views
Tutorial:
Differentially expressed gene analysis in Python with omicverse
RNA-seq
Python
4 months ago by
Starlitnightly
• 0
19
votes
13
replies
7.9k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 27 days ago by
jude
• 0 • written 17 months ago by
ATpoint
78k
2
votes
0
replies
2.9k
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 4 months ago by
Ram
41k • written 4 months ago by
Ming Tommy Tang
★ 3.6k
18
votes
7
replies
6.0k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 4 months ago by
ATpoint
78k • written 3.7 years ago by
colindaven
5.7k
3
votes
2
replies
656
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC
transcription
factor
ChIP-seq
4 months ago by
Ming Tommy Tang
★ 3.6k
88
votes
22
replies
83k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 4 months ago by
sifa.khan
• 0 • written 5.4 years ago by
otwtgin2010
▴ 580
2
votes
0
replies
334
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 4 months ago by
Ram
41k • written 4 months ago by
Ming Tommy Tang
★ 3.6k
4
votes
0
replies
516
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
5 months ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
438
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 5 months ago by
Ram
41k • written 5 months ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
435
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
5 months ago by
sinha.shriprakash
▴ 20
1
vote
2
replies
628
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 5 months ago by
Ram
41k • written 5 months ago by
Ming Tommy Tang
★ 3.6k
1
vote
0
replies
466
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 5 months ago by
Ram
41k • written 5 months ago by
Ming Tommy Tang
★ 3.6k
2
votes
0
replies
517
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
5 months ago by
Ming Tommy Tang
★ 3.6k
1
vote
0
replies
463
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
5 months ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
510
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
5 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
516
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 5 months ago by
Ram
41k • written 5 months ago by
Coremine Medical
▴ 20
3
votes
0
replies
776
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
6 months ago by
Ming Tommy Tang
★ 3.6k
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 6 months ago by
GenoMax
136k • written 10.0 years ago by
Obi Griffith
20k
2
votes
0
replies
853
views
Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 8 months ago by
ATpoint
78k • written 8 months ago by
Simon
▴ 40
1
vote
0
replies
590
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 22 days ago by
Ram
41k • written 8 months ago by
Milad
▴ 10
3
votes
2
replies
2.5k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 6 months ago by
Ram
41k • written 6.6 years ago by
jnowacki
▴ 100
7
votes
3
replies
2.0k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 7 months ago by
Randy H
▴ 110 • written 15 months ago by
Kevin Blighe
86k
3
votes
3
replies
2.4k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC
TCGABiolinks
STAR
updated 9 months ago by
Ram
41k • written 19 months ago by
DareDevil
★ 3.3k
2
votes
0
replies
934
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 16 days ago by
Ali
• 0 • written 10 months ago by
firestar
★ 1.6k
11
votes
7
replies
1.9k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
8 months ago by
barslmn
★ 2.0k
2
votes
1
reply
1.9k
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 10 months ago by
Pierre Lindenbaum
158k • written 10 months ago by
barslmn
★ 2.0k
4
votes
2
replies
1.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
4 months ago by
Dr.Animo
▴ 80
383 results • Page
1 of 8
Recent Votes
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
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