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913 results • Page
1 of 19
Sort: Votes
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Views
Votes
Replies
18
votes
4
replies
8.1k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 25 days ago by
Ram
38k • written 9.6 years ago by
user
▴ 930
14
votes
5
replies
2.7k
views
bioinformatics basic training
genome
updated 11 days ago by
Ram
38k • written 8.3 years ago by
f.muoghalu
• 0
10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 3 days ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
10
votes
15
replies
5.2k
views
convert fasta/gb to vcf
fasta
vcf
genbank
gff
updated 2 days ago by
Ram
38k • written 4.5 years ago by
marongiu.luigi
▴ 670
9
votes
16
replies
2.9k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 2 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
9
votes
20
replies
3.2k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 2 days ago by
Ram
38k • written 4.6 years ago by
marongiu.luigi
▴ 670
8
votes
12
replies
2.4k
views
Use BLAST Command Line Applications to run a folder of many sequences against a database
BLAST
updated 7 days ago by
Ram
38k • written 19 months ago by
daver.v
▴ 30
8
votes
25
replies
1.9k
views
construction of a database
sql
noSQL
neo4j
database
updated 3 days ago by
Ram
38k • written 22 months ago by
Debut
▴ 20
7
votes
6
replies
1.3k
views
How to get/calculate coverage of a gene using bed file?
bed
coverage
gene
updated 2 days ago by
Ram
38k • written 16 months ago by
Nikhil
▴ 10
7
votes
4
replies
1.2k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 10 days ago by
Ram
38k • written 4.7 years ago by
healing80
• 0
7
votes
4
replies
1.7k
views
useful and freely available softwares for Bioinformatics
software
updated 7 days ago by
Ram
38k • written 8.0 years ago by
Mo
▴ 920
7
votes
10
replies
1.1k
views
col as names [solved]
R
updated 7 days ago by
Ram
38k • written 4.0 years ago by
demoraesdiogo2017
▴ 90
6
votes
11
replies
719
views
Calculate RPKM
RPKM
4 days ago by
Chris
▴ 70
6
votes
13
replies
625
views
Error with STAR
STAR
updated 15 days ago by
Ram
38k • written 18 days ago by
Chris
▴ 70
6
votes
12
replies
1.2k
views
VCF files 101 - for people from non Bioinformatics Background
vcf
sequencing
genome
variant-calling
updated 11 days ago by
Ram
38k • written 2.6 years ago by
akshaykum684
▴ 20
6
votes
7
replies
825
views
to mark the duplicates
Assembly
updated 11 days ago by
Ram
38k • written 3.8 years ago by
manubiomed20
▴ 10
6
votes
3
replies
3.1k
views
Comment On The Introduction Of A Bioinformatics Paper
publication
bayesian-model
updated 18 days ago by
Ram
38k • written 9.0 years ago by
Faheemmitha
▴ 210
6
votes
6
replies
910
views
RNA-seq pipeline for degraded RNA
RNA-Seq
degraded
pipeline
alignment
updated 19 days ago by
yussab
▴ 80 • written 2.2 years ago by
oludhe
▴ 60
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 4 days ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
6
votes
6
replies
3.5k
views
Already Working In The Field Of Bioinformatics With A Bachelors, Is A Masters Degree Worth The Time?
masters
career
updated 24 days ago by
Ram
38k • written 9.5 years ago by
ashah90
▴ 30
6
votes
12
replies
1.1k
views
Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
r
biomarker
updated 7 days ago by
Ram
38k • written 4.2 years ago by
english.server
▴ 290
5
votes
6
replies
613
views
Filter out Bam not overlapping with Bed File (keeping a read and its mate)?
mates
bed
bam
samtools
11 days ago by
Eliveri
▴ 340
5
votes
6
replies
430
views
I can not allocate ram memory for WSL2
WSL2
10 days ago by
ailton
• 0
5
votes
4
replies
1.7k
views
MyVariant.info fields descriptions?
genome
snp
variant
updated 1 day ago by
Ram
38k • written 6.9 years ago by
Nolwenn Lavielle
▴ 90
5
votes
6
replies
2.9k
views
Changes log2FC values of DESeq2
log2FC
DESeq2
updated 1 day ago by
Ram
38k • written 5.2 years ago by
realnewbie
▴ 30
5
votes
11
replies
3.0k
views
Convert Plink to Arlequin
software-error
plink
Arlequin
PGDSpider
updated 10 days ago by
Ram
38k • written 4.9 years ago by
HG
▴ 30
5
votes
4
replies
506
views
Converting Bam file to Fasta (Zipped)
samtools
bamtofastq
bedtools
paired
11 days ago by
Eliveri
▴ 340
4
votes
7
replies
2.0k
views
How to move the files from sub folder and sub-sub folders into one other folder?
bash
updated 2 days ago by
Ram
38k • written 21 months ago by
mathavanbioinfo
▴ 70
4
votes
4
replies
2.5k
views
What Statistical Test Is Appropriate When Comparing Rna-Seq Data Obtained From Biological Replicates Mapped To Different Genomes
RNA-seq
updated 29 days ago by
Ram
38k • written 10.2 years ago by
xs57
▴ 20
4
votes
3
replies
182
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
1 day ago by
luzglongoria
▴ 40
4
votes
5
replies
520
views
Need help to perform survival analysis
survival
analysis
mirna
updated 12 days ago by
Mensur Dlakic
★ 23k • written 13 days ago by
Bhanu
• 0
4
votes
3
replies
679
views
Bioinformatics courses online?
courses
updated 17 days ago by
Ram
38k • written 19 months ago by
valentinavan
▴ 50
4
votes
1
reply
312
views
Batch effect correction methods (Seurat v3, Harmony, fastMNN, Liger)
integration
Batch
seurat
fastMNN
Harmony
25 days ago by
re_raz
▴ 50
4
votes
2
replies
905
views
Convert BAM files to GENOMEDATA files
BAM
genomedata
updated 2 days ago by
Ram
38k • written 4.9 years ago by
Armand
• 0
4
votes
9
replies
6.7k
views
bcftools consensus command
vcf
bcftools
updated 2 days ago by
Ram
38k • written 3.2 years ago by
Begonia_pavonina
▴ 90
3
votes
5
replies
1.9k
views
Cellranger count command for single end fastq
RNA-Seq
sequencing
updated 24 days ago by
Ram
38k • written 2.3 years ago by
sidrah.maryam
▴ 40
3
votes
1
reply
2.1k
views
reference and effective allele
snp
updated 15 days ago by
Ram
38k • written 8.3 years ago by
alex.crimi
• 0
3
votes
4
replies
461
views
Genome Reference Consortium Human Build - Transcriptome Size Query
GRC
updated 7 days ago by
Ram
38k • written 10 months ago by
Oligo96
• 0
3
votes
2
replies
504
views
[bam-readcount v.0.8.0] Fail to open BAM file –q
bam-readcount
BAM
updated 2 days ago by
Ram
38k • written 22 months ago by
vanessagpds
▴ 10
3
votes
4
replies
1.4k
views
How to get regions with mapped reads
bed
bam
RNA-Seq
bedtools
updated 2 days ago by
Ram
38k • written 4.5 years ago by
nanoide
▴ 100
3
votes
4
replies
255
views
Creating sample groups from a combination of genes for survival analysis
Survival
3 days ago by
krushnach80
★ 1.1k
3
votes
4
replies
326
views
How much reads per cell for fusion detection with Nanopore ?
single-cell
fusion
nanopore
1 day ago by
Evan
▴ 180
3
votes
6
replies
1.7k
views
Methods and type datastructures use by Splign?
data-structure
splign
updated 3 days ago by
Ram
38k • written 6.4 years ago by
Esaie
▴ 160
3
votes
3
replies
395
views
SamSort gatk invalid argument / no space left on disk
picard
gatk
samsort
nextflow
11 days ago by
Eliveri
▴ 340
3
votes
0
replies
1.8k
views
Combined VCF file for all GTEx genotype calls?
GTExv7
GTEx
Genotype
dbGap
VCF
updated 2 days ago by
Ram
38k • written 5.5 years ago by
django.waddle
▴ 60
3
votes
6
replies
4.3k
views
Why Do I Get A Makeblastdb Error: File Does Not Match Input Format Type, Default Input Type Is Fasta
genomics
blast-plus
updated 23 days ago by
Ram
38k • written 9.3 years ago by
alok.helix
▴ 120
3
votes
4
replies
479
views
Changing Temporary File Location for Local BLASTP to nr Database
protein
blast
nr
updated 4 days ago by
Ram
38k • written 10 weeks ago by
katieostrouchov
▴ 20
3
votes
2
replies
204
views
correlations in R
cor
R
2 days ago by
rene.j.erhardt
▴ 20
3
votes
3
replies
336
views
Retrieving information from FASTA file
NGS
FASTA
VCF
updated 3 days ago by
Ram
38k • written 12 months ago by
Maryam
▴ 10
3
votes
2
replies
347
views
A way to find which genome builds a package supports
Bioconductor
genome
R
build
updated 13 days ago by
ATpoint
70k • written 14 days ago by
dshcherbo
• 0
913 results • Page
1 of 19
Recent Votes
A: microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
Converting SNP from chr:pos to rs number using PLINK?
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
Answer: Cellranger sequencing
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
Answer: multiallelic variants
Comment: Python formatting when visualizing Primer3-py dimers
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Recent Replies
Comment: Remove part of headers in FASTA file
by
Pierre Lindenbaum
153k
Use `cut -d ' '`
Answer: Problem running interproscan-5.15-54.0 for protein sequences
by
Pratyay
• 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices.
by
krushnach80
★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices.
by
jose.sgomez94
• 0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2
by
FrankStarling
▴ 50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html …
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
Adaline.D
• 0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power. (1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
LChart
2.2k
Short answer: use LIMMA Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴ 30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction
by
dthorbur
▴ 420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Comment: chloroplast genome gaps
by
ugur
• 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing
by
ATpoint
70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ?
by
Mensur Dlakic
★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction
by
GenoMax
127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers
by
Wayne
★ 1.7k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
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