Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
98 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
239
votes
176
replies
96k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 12 months ago by
Ram
43k • written 8.8 years ago by
TriS
★ 4.7k
102
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 5 weeks ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
88k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
24 days ago by
Kevin Blighe
88k
150
votes
70
replies
51k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.5 years ago by
Kevin Blighe
88k
90
votes
48
replies
34k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.4 years ago by
vimalkvn
▴ 320
50
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 7 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 9 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 10 months ago by
amziepickles
• 0 • written 8.2 years ago by
Obi Griffith
20k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
21
votes
26
replies
9.8k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 9 weeks ago by
Yao
▴ 30 • written 4.5 years ago by
Juke34
8.6k
87
votes
24
replies
24k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 4 weeks ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
93
votes
23
replies
93k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 4 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
39
votes
16
replies
37k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.8 years ago by
lavinia.gordon
▴ 160
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
65
votes
15
replies
15k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 12 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 11 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 29 days ago by
ATpoint
82k • written 4 weeks ago by
BioinfGuru
★ 1.7k
21
votes
13
replies
11k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 6 months ago by
jude
• 0 • written 23 months ago by
ATpoint
82k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 9 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
19
votes
7
replies
6.7k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 months ago by
ATpoint
82k • written 4.2 years ago by
colindaven
6.4k
10
votes
6
replies
4.2k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 7 weeks ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
88k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 8 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
1
vote
5
replies
678
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
5
votes
5
replies
676
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 16 days ago by
Mbofire
• 0 • written 24 days ago by
Ming Tommy Tang
★ 3.9k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 12 months ago by
Ram
43k • written 5.6 years ago by
elia.brodsky
▴ 340
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 12 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
1
vote
4
replies
3.4k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 12 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
10
votes
4
replies
5.7k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
9 months ago by
Hamid Ghaedi
3.2k
0
votes
4
replies
779
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
6 months ago by
Coremine Medical
▴ 20
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 4 weeks ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
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 9 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
3
votes
3
replies
1.2k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 4 months ago by
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
3
replies
651
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
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
10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
2
replies
1.6k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 11 months ago by
Ram
43k • written 20 months ago by
Sandhiya
▴ 20
6
votes
2
replies
5.1k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by
GenoMax
142k
1
vote
2
replies
903
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
3
votes
2
replies
582
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by
ATpoint
82k • written 4 months ago by
Julia Ma
▴ 120
8
votes
2
replies
1.2k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 9 months ago by
Ram
43k • written 9 months ago by
carlopecoraro2
★ 2.5k
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
7
votes
1
reply
209
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 12 days ago by
dariober
14k • written 12 days ago by
nhaus
▴ 360
2
votes
1
reply
480
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
587
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
316
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
568
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 8 months ago by
ATpoint
82k • written 8 months ago by
JC
▴ 30
1
vote
1
reply
381
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
3
votes
1
reply
658
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
3
votes
1
reply
3.5k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 3 months ago by
MaxF
▴ 120 • written 2.8 years ago by
Kevin Blighe
88k
98 results • Page
1 of 2
Recent Votes
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: How to add Ensembl id to cluster.markers in Seurat
How to add Ensembl id to cluster.markers in Seurat
Recent Locations •
All
South Korea,
8 minutes ago
United States,
9 minutes ago
Australia,
12 minutes ago
India,
17 minutes ago
United States,
19 minutes ago
United States,
22 minutes ago
United States,
33 minutes ago
Recent Awards •
All
Scholar
to
Pierre Lindenbaum
161k
Voter
to
Sara
▴ 30
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
Scholar
to
jv
★ 1.8k
Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files
by
Tommaso
• 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot
by
Ghada
• 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Hi Pierre, I am attempting to run this code and am running into this error: (jvar) $ jvarkit vcffilterjdk -f biostar.code Dart_VCF2_Or…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Traffic: 1077 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6