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384 results • Page
2 of 8
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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
2
votes
0
replies
1.0k
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
R
data-mining
Gene-pathway-enrichment
RNA-Seq
updated 5 months ago by
Ram
41k • written 11 months ago by
Novogene
▴ 360
1
vote
0
replies
2.3k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 5 months ago by
Ram
41k • written 11 months ago by
Novogene
▴ 360
5
votes
0
replies
1.2k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 5 months ago by
Ram
41k • written 11 months ago by
Novogene
▴ 360
6
votes
0
replies
3.4k
views
Tutorial:
How to download GEO data Quickly and easily
geo
RNA-Seq
R
data-mining
9 months ago by
Novogene
▴ 360
50
votes
1
reply
7.9k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 10 months ago by
Ram
41k • written 3.2 years ago by
ATpoint
78k
1
vote
3
replies
803
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbssampling
splice
8 months ago by
barslmn
★ 2.0k
73
votes
60
replies
26k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 10 months ago by
Ram
41k • written 6.2 years ago by
Kevin Blighe
86k
14
votes
31
replies
6.1k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 9 months ago by
Ram
41k • written 4.3 years ago by
Juke34
8.4k
1
vote
2
replies
1.3k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 5 months ago by
Ram
41k • written 14 months ago by
Sandhiya
▴ 20
1
vote
0
replies
717
views
Tutorial:
Making LDA Score plot
LDA
metagenomics
14 months ago by
rohitsatyam102
▴ 780
132
votes
123
replies
35k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 8 months ago by
1769mkc
★ 1.1k • written 5.1 years ago by
Kevin Blighe
86k
11
votes
7
replies
9.9k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 6 months ago by
Ram
41k • written 2.8 years ago by
Novogene
▴ 360
15
votes
1
reply
3.5k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 15 months ago by
Assa Yeroslaviz
★ 1.8k • written 23 months ago by
dariober
14k
84
votes
21
replies
20k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 9 months ago by
Ram
41k • written 3.2 years ago by
Hamid Ghaedi
3.1k
27
votes
0
replies
3.4k
views
Tutorial:
Building Docker images
singularity
docker
container
16 months ago by
ATpoint
78k
2
votes
1
reply
49k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 16 months ago by
LauferVA
3.8k • written 16 months ago by
kodwings
▴ 20
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 6 months ago by
adelheidkratzer
• 0 • written 5.5 years ago by
egeulgen
★ 1.3k
85
votes
2
replies
57k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by
Ram
41k • written 10.5 years ago by
Eric Normandeau
11k
15
votes
5
replies
12k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 9 months ago by
Ram
41k • written 6.0 years ago by
ahmad mousavi
▴ 770
39
votes
8
replies
12k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 9 months ago by
Ram
41k • written 3.2 years ago by
Hamid Ghaedi
3.1k
3
votes
2
replies
2.4k
views
Tutorial:
Running fastq_screen on your data
fastqscreen
20 months ago by
rohitsatyam102
▴ 780
7
votes
14
replies
3.3k
views
6 follow
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by
Angelina_G
• 0 • written 21 months ago by
thehung92phuyen
▴ 30
75
votes
14
replies
15k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 10 months ago by
Ram
41k • written 10.6 years ago by
Medhat
9.7k
28
votes
13
replies
12k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 22 months ago by
liorglic
★ 1.3k • written 2.2 years ago by
Istvan Albert
99k
4
votes
13
replies
12k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 5 months ago by
Ram
41k • written 4.8 years ago by
jaybee
▴ 140
16
votes
9
replies
6.3k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 18 months ago by
dk0319
▴ 70 • written 2.0 years ago by
Barry Digby
★ 1.3k
0
votes
0
replies
11k
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
23 months ago by
Wayne
★ 1.8k
12
votes
4
replies
5.1k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 10 months ago by
Ram
41k • written 2.8 years ago by
garden_giessen
▴ 130
29
votes
10
replies
74k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 9 months ago by
Ram
41k • written 2.7 years ago by
Nitin Narwade
★ 1.5k
44
votes
6
replies
23k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 22 months ago by
cameron.cowan
▴ 40 • written 2.7 years ago by
rpolicastro
12k
148
votes
70
replies
48k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 3 months ago by
Raheleh
▴ 260 • written 6.0 years ago by
Kevin Blighe
86k
15
votes
2
replies
1.9k
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 14 months ago by
brunobsouzaa
▴ 820 • written 2.2 years ago by
nhaus
▴ 280
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 months ago by
Ram
41k • written 11.2 years ago by
Obi Griffith
20k
6
votes
2
replies
1.5k
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
2.3 years ago by
Kevin Blighe
86k
0
votes
0
replies
1.1k
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
2.3 years ago by
mo
• 0
2
votes
0
replies
2.8k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
2.4 years ago by
Kevin Blighe
86k
45
votes
2
replies
36k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 9 months ago by
Ram
41k • written 11.7 years ago by
MSU course 2011
▴ 540
95
votes
105
replies
41k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 9 months ago by
Ram
41k • written 5.3 years ago by
Kevin Blighe
86k
0
votes
0
replies
1.0k
views
Tutorial:
Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation
bioimaging
SLURM
health
2.5 years ago by
Erin Haskell | ELIXIR
▴ 470
1
vote
0
replies
1.2k
views
Tutorial:
Slurm and parallelization
slurm
2.5 years ago by
Juke34
8.4k
1
vote
0
replies
1.2k
views
Tutorial:
How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo
cytoscape
2.5 years ago by
Pratik
▴ 980
13
votes
1
reply
2.7k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 2.5 years ago by
jared.andrews07
★ 16k • written 2.5 years ago by
Kevin Blighe
86k
117
votes
66
replies
44k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 9 months ago by
Ram
41k • written 5.4 years ago by
ATpoint
78k
4
votes
0
replies
1.2k
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
2.5 years ago by
pbpanigrahi
▴ 420
0
votes
1
reply
994
views
Tutorial:
Add Customized Filters in GDC
gdc
updated 2.5 years ago by
cpad0112
21k • written 2.5 years ago by
Zhenyu Zhang
★ 1.1k
65
votes
26
replies
13k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 9 months ago by
Ram
41k • written 4.8 years ago by
finswimmer
16k
12
votes
20
replies
13k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 9 months ago by
Ram
41k • written 4.5 years ago by
jared.andrews07
★ 16k
4
votes
2
replies
2.3k
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0
beagle
updated 9 months ago by
Ram
41k • written 4.5 years ago by
Shicheng Guo
★ 9.3k
51
votes
14
replies
80k
views
10 follow
Tutorial:
Using R in Conda
R
updated 9 months ago by
Ram
41k • written 3.4 years ago by
rohitsatyam102
▴ 780
384 results • Page
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Recent Votes
Comment: GATK GetPileupSummaries Java heap space
Answer: How to subtract variants from one VCF file to another?
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Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq
by
rpolicastro
12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
RCMC
• 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
how about using the bed file of your targets....
Answer: LCA from BLAST output
by
Dunois
★ 2.4k
You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] . [1]: https:/…
Comment: autodock vina on mac
by
iamsmor
• 0
thank you but ı am already follow this tutorial steps but at mgltools steps at the page but ı dont undertsand there isnot no enough explana…
Comment: How to create interval list from reference fasta or dict file?
by
Manuel Sokolov Ravasqueira
▴ 100
Hello @MatthewP , were you able to that for a fasta file for example? If you have a fasta file containing a targeted region, how to you ge…
Comment: WGCNA Dendrogram Branch missing from modules
by
andres.firrincieli
3.5k
I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
Comment: LCA from BLAST output
by
Michael
53k
If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
Comment: Is GeSeq currently unavailable?
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GenoMax
136k
Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
Comment: Alternative to Gentrome?
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GenoMax
136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
Comment: Java class error message when using BBDuk
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GenoMax
136k
> I have cloned the bbmap Git Hub You are not using official repository then. BBMap is available from [**SourceForge**][1] or Bitbucket…
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