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143 results • Page
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239
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176
replies
95k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 16 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
8 hours ago by
Kevin Blighe
87k
149
votes
70
replies
50k
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 6.4 years ago by
Kevin Blighe
87k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 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 5.8 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 6.3 years ago by
vimalkvn
▴ 320
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 27 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
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 8.1 years ago by
Obi Griffith
20k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 6 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 5 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 7 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
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
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 11 months ago by
GenoMax
141k • written 10.4 years ago by
Obi Griffith
20k
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
141k • written 3.7 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 5 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 months ago by
Ram
43k • written 5.5 years ago by
finswimmer
16k
5
votes
13
replies
1.1k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 4 days ago by
ATpoint
82k • written 5 days ago by
BioinfGuru
★ 1.7k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 6 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
21
votes
13
replies
10k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 5 months ago by
jude
• 0 • written 22 months ago by
ATpoint
82k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
12
votes
11
replies
7.5k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 11 months ago by
Ram
43k • written 7.1 years ago by
CandiceChuDVM
★ 2.4k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
11
votes
7
replies
14k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 11 months ago by
Ram
43k • written 6.6 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 3.1 years ago by
Novogene
▴ 420
19
votes
7
replies
6.5k
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
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 29 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 11 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
1
vote
5
replies
607
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
4
replies
724
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
5 months ago by
Coremine Medical
▴ 20
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 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 11 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
2
votes
3
replies
2.7k
views
Tutorial:
It's about the journey, and not the destination
R
network
updated 11 months ago by
Ram
43k • written 7.0 years ago by
theobroma22
★ 1.2k
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 6 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
1.1k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 3 months ago by
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
3
replies
559
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
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
3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 11 months ago by
Ram
43k • written 6.4 years ago by
bernatgel
★ 3.4k
6
votes
2
replies
4.2k
views
Tutorial:
GATK method for filtering vcf lines using GT values at all or multisample level.
genome
vcf
genotype
variant-filtration
updated 11 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
1
vote
2
replies
872
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
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Shicheng Guo
★ 9.4k
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 7 months ago by
GenoMax
141k • written 4.0 years ago by
ATpoint
82k
143 results • Page
1 of 3
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Assa Yeroslaviz
★ 1.8k
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to
Keem Uarren Eiryll
• 0
Centurion
to
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Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
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