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98 results • Page
1 of 2
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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
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
102
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 6 weeks ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
88k
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
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
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
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
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
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
25 days ago by
Kevin Blighe
88k
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
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
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
50
votes
30
replies
12k
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
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
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
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
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
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
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
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
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
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
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
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 6.3 years ago by
Kevin Blighe
88k
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
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
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 5.3 years ago by
jaybee
▴ 170
7
votes
1
reply
214
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 13 days ago by
dariober
14k • written 13 days ago by
nhaus
▴ 360
7
votes
0
replies
618
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
9 months ago by
barslmn
★ 2.2k
6
votes
0
replies
588
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by
zx8754
11k • written 3 months ago by
Ming Tommy Tang
★ 3.9k
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
6
votes
1
reply
491
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
5
votes
5
replies
680
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 17 days ago by
Mbofire
• 0 • written 25 days ago by
Ming Tommy Tang
★ 3.9k
5
votes
13
replies
2.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 weeks ago by
ATpoint
82k • written 4 weeks ago by
BioinfGuru
★ 1.7k
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 11 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
4
votes
0
replies
795
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
2
replies
3.0k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
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
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 9 months ago by
Ming Tommy Tang
★ 3.9k
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 6.1 years ago by
chen
★ 2.5k
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
1
reply
659
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
0
replies
765
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
11 months ago by
Ming Tommy Tang
★ 3.9k
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
3
votes
2
replies
583
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
3
votes
0
replies
257
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
12 weeks ago by
Novogene
▴ 420
2
votes
0
replies
1.3k
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
R
data-mining
Gene-pathway-enrichment
RNA-Seq
updated 11 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
2
votes
0
replies
1.4k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 12 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
2
votes
0
replies
446
views
Tutorial:
Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA
RNA-seq
updated 4 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
2
votes
0
replies
491
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
98 results • Page
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Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
A: Bcftools merge taking too much time and producing large file
Answer: Kraken2 database
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Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
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Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
ojaswinipandey
• 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
Dave Carlson
★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool
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Ram
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Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
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This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
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Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results
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GenoMax
142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
by
Anita
• 0
Great, thank you!
Comment: Filter Genome for Specific Sites
by
Anita
• 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
Comment: Filter Genome for Specific Sites
by
Pierre Lindenbaum
161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
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