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1,000 results • Page
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Job:
Postdoctoral Research Associate in Computational Biology
engineering
learning
protein
computational
machine
biology
deep
44 minutes ago by
DrStracquadanio
▴ 10
0
votes
1
reply
76
views
Biopython intron-exon boundary nucleotide frequencies
python
arrays
Biopython
updated 38 minutes ago by
Joe
20k • written 4 days ago by
ash.maladec
• 0
5
votes
6
replies
149
views
Forum:
PC build for Nanopore data analysis
PC
pipeline
sequencing
python
nanopore
updated 1 hour ago by
Jean-Karim Heriche
25k • written 7 hours ago by
stan.aanhane
▴ 30
0
votes
1
reply
699
views
MG RAST for Eukaryota
MG-RAST
Eukaryota
metagenomics
functions
KEGG
updated 1 hour ago by
young_bioinformatician
▴ 170 • written 22 months ago by
TomM
• 0
0
votes
5
replies
51
views
bcftools stats: definition of indel type
vcf
bcftools
1 hour ago by
WouterDeCoster
46k
0
votes
6
replies
84
views
arrange samples in same order in rows and column in R
R
statistics
1 hour ago by
Bioinfonext
▴ 380
670
votes
160
replies
84k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 5 weeks ago by
Biostar
740 • written 5.5 years ago by
Istvan Albert
93k
0
votes
1
reply
38
views
BED file from GSEA gene set
ChIP-seq
BED
ChIP
bioinformatics
GSEA
file
updated 59 minutes ago by
ATpoint
61k • written 3 hours ago by
2138493o
▴ 20
1
vote
3
replies
91
views
Recent alternative to LalnView
Synteny
Evolution
Genome
Alignment
3 hours ago by
maxime.policarpo
▴ 170
0
votes
3
replies
83
views
Which data files are required to find GWAS summary statistics?
plink
updated 2 hours ago by
4galaxy77
★ 1.7k • written 3 hours ago by
Raju
• 0
26
votes
4
replies
12k
views
Tool:
Plotting GSEA output in R
javaGSEA
GSEA
RNA-Seq
plot
Tool
updated 3 hours ago by
valentinafu
• 0 • written 5.8 years ago by
thomaskuilman
▴ 820
0
votes
2
replies
103
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
DifferentialExpression
RNAseq
R
Limma
updated 1 hour ago by
Gordon Smyth
★ 4.4k • written 5 hours ago by
dzisis1986
▴ 40
15
votes
14
replies
5.4k
views
Execute commands in Bash Chunk in Rmarkdown
vcftools
samtools
rmarkdown
rstudio
updated 5 hours ago by
ariel
▴ 190 • written 2.6 years ago by
M.O.L.S
▴ 40
2
votes
10
replies
176
views
Strange Trimmomatic behavior
Trimmomatic
updated 1 hour ago by
lieven.sterck
13k • written 5 hours ago by
ctdarwell
• 0
0
votes
3
replies
113
views
How to install PEERTOOLS in a cluster?
linux
Peertools
GWAS
predictdb
unix
updated 3 hours ago by
solomoncharles77
▴ 90 • written 5 hours ago by
fernandogs97
• 0
0
votes
0
replies
25
views
WES -> recalibration matrix and Deduplication matrix reads number is very strange.
matrix
recal
dedup
reads
6 hours ago by
jk.kim
• 0
3
votes
1
reply
83
views
How to delete Duplicate snps in plink 1.9
duplicate
snp
plink
updated 6 hours ago by
zx8754
11k • written 10 hours ago by
xuyang
▴ 10
0
votes
0
replies
39
views
Palimpsest deconvolution_fit() problem
palimpsest
de
mutation
signature
extraction
novo
9 hours ago by
15927207765
• 0
0
votes
0
replies
55
views
Job:
Scientist, Simons Collaboration on the Global Brain
Neuroscience
11 hours ago by
simonsF.careers
• 0
1
vote
1
reply
125
views
convert csv to fasta format using python
python
updated 3 hours ago by
Joe
20k • written 11 hours ago by
Abdellrhmanakl
• 0
0
votes
0
replies
66
views
Read counts an order of magnitude higher on one chromosome
novaseq
alignment
Rad-seq
sequencing
demultiplex
11 hours ago by
Samuel
• 0
0
votes
5
replies
177
views
EGA (ENA) database wont accept fastq files
ENA
EGA
fastq
updated 3 hours ago by
lieven.sterck
13k • written 12 hours ago by
heskett
▴ 80
0
votes
4
replies
176
views
Split fastq files
Fastq
split
novaseq
updated 2 hours ago by
GenoMax
115k • written 14 hours ago by
zeina-younes
• 0
0
votes
0
replies
43
views
qPCR Assay plot
barplot
qpcr
R
15 hours ago by
Maria17
• 0
2
votes
2
replies
143
views
Adding a new protein to similarity matrix based on sequence alignment
protein
similarity
sequence
R
msa
13 hours ago by
27b99607
• 0
0
votes
4
replies
138
views
Using fastq-mcf tool
Genomics
updated 6 hours ago by
Pierre Lindenbaum
145k • written 15 hours ago by
aranyak111
• 0
0
votes
1
reply
156
views
Find markers from multiple groups using bulk RNA-seq data
RNA-seq
findMarkers
bulk
DEG
updated 16 hours ago by
Chris S.
▴ 320 • written 8 weeks ago by
ccfpwll
• 0
0
votes
2
replies
74
views
Error in GATK haplotypecaller running
GATK
updated 16 hours ago by
Ram
36k • written 16 hours ago by
Azhar Jameel
• 0
0
votes
1
reply
1.1k
views
AutoDock needs the extension of the docking parameter file to be ".dpf"?
autodock
docking
autogrid
updated 17 hours ago by
Dr. Osuolale
• 0 • written 2.9 years ago by
arunsaikirans
• 0
2
votes
7
replies
178
views
error while using cyvcf2 to parse the vcf file
error
vcf
cyvcf2
htslib
parsing
15 hours ago by
rheab1230
▴ 50
0
votes
0
replies
45
views
CNV and DUP in vcf files Gnomad database
dup
cnv
gnomad
vcf
17 hours ago by
arya.sagittarius
• 0
6
votes
4
replies
190
views
Forum:
How to learn bioinformatics?
bioinformatics
updated 16 hours ago by
Marco Pannone
▴ 240 • written 19 hours ago by
sakichwan
▴ 10
0
votes
1
reply
63
views
counting snps from alternative allele using tsv format
python
updated 17 hours ago by
Pierre Lindenbaum
145k • written 17 hours ago by
Abdellrhmanakl
• 0
2
votes
2
replies
66
views
What do they mean by "multidomain" and "multimetric"?
protein
protein-structure
protein-structure-prediction
17 hours ago by
user366312
▴ 10
0
votes
2
replies
113
views
R, group data based on names and sum each group
manipulation
R
data
updated 14 hours ago by
cpad0112
20k • written 18 hours ago by
mthm
▴ 40
0
votes
5
replies
121
views
blast with multithreads is much slower
blast
16 hours ago by
biobiu
▴ 130
0
votes
0
replies
72
views
What conclusions can I draw from a Procrustes Superimposition Test?
Multivariate
Statistics
Procrustes
Correlation
14 hours ago by
dch014
• 0
0
votes
7
replies
198
views
GSEA not returning significant gene sets
GSEA
updated 6 hours ago by
ATpoint
61k • written 19 hours ago by
jabbari.parnian
▴ 20
0
votes
1
reply
64
views
bcl2fastq error: Barcode lengths in the sample sheet do not match those in --use-bases-mask
cellranger
bcl2fastq
CITE
mkfastq
CITE-seq
updated 17 hours ago by
GenoMax
115k • written 19 hours ago by
coteparker
• 0
0
votes
7
replies
163
views
6 follow
How to create kallisto index that does not include ribosomal genes
rna-seq
enseml
bioinformatics
kallisto
updated 6 hours ago by
ATpoint
61k • written 20 hours ago by
bioinfo
▴ 10
0
votes
3
replies
103
views
SRR sample ID
TCGAbiolinks
RNA-seq
sampleID
R
cancer
programming
updated 16 hours ago by
Hamid Ghaedi
★ 2.5k • written 19 hours ago by
mahsa
• 0
2
votes
2
replies
153
views
Donwloading latest version of Mouse ref genome
musculus.
Reference
Ensembl
Mus
genome
updated 20 hours ago by
vkkodali_ncbi
★ 3.1k • written 1 day ago by
salman_96
▴ 50
0
votes
0
replies
40
views
guppy_barcoder - demultiplex- custom barcodes
nanopore
guppy
demultiplex
updated 21 hours ago by
Ram
36k • written 21 hours ago by
henry-keen
▴ 20
1
vote
1
reply
80
views
DESeq2 and WGCNA
DESeq2
RNAseq
WGCNA
updated 5 hours ago by
Basti
▴ 340 • written 21 hours ago by
pthom010
▴ 20
2
votes
5
replies
361
views
How to access the ACLAME server?
ACLAME
21 hours ago by
cloredana20
▴ 10
0
votes
0
replies
41
views
Inferring GRN without transcription factor motif
scenic
GRN
cell
single
21 hours ago by
William
• 0
2
votes
2
replies
98
views
bcl2fastq with unique dual indexing
demultiplexing
UDI
DNAseq
sequencing
5 hours ago by
ginlucks
▴ 10
2
votes
1
reply
63
views
Msigdb GO:BP
msigdb
updated 21 hours ago by
igor
12k • written 22 hours ago by
AriBo
• 0
0
votes
3
replies
142
views
How to search and identify the function of DEGs
function
functional
annoatation
DEGs
updated 19 hours ago by
Marco Pannone
▴ 240 • written 1 day ago by
Roy.anupama11
• 0
1
vote
3
replies
160
views
Can I compare different RNAseq experiment DEG lists to see which experiments are the most similar?
DEG
lists
Comparision
RNAseq
updated 20 hours ago by
rpolicastro
8.2k • written 22 hours ago by
rachel.walters.18
• 0
1,000 results • Page
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Recent Votes
Answer: Retrieve All Genes Associated With A Go Term
Comment: awk command help
A: Table browser +/- 2Kb of TSS export
C: Pca From Vcf Files
A: EdgeR analysis with CPM normalzed counts
Comment: PC build for Nanopore data analysis
Comment: PC build for Nanopore data analysis
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Recent Replies
Answer: Biopython intron-exon boundary nucleotide frequencies
by
Joe
20k
Eukaryote genomics is not a area of expertise for me so apologies if I miss some subtlety with the exons/introns here, but if the tasks is …
Comment: BED file from GSEA gene set
by
ATpoint
61k
What exactly is the question? Do you need code to make a BED file, and if so based on what? Gene symbols, coordinates of peaks? Please add …
Comment: Strange Trimmomatic behavior
by
lieven.sterck
13k
can you first confirm it is GBS data we're talking about here?
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
This also shows error, Is there any way in R to arrange samples in same rows/column? fit <- lmFit(t(mval), var) Error in lmFit(t(mval),…
Comment: PC build for Nanopore data analysis
by
Jean-Karim Heriche
25k
I assumed that this was already covered because of the mention of > a pipeline for the data that is subsequently generated
Answer: PC build for Nanopore data analysis
by
GenoMax
115k
I assume you are referring to MinION sequencing since other larger ONT sequencers are supplied with built in compute for doing some of the …
Comment: PC build for Nanopore data analysis
by
GenoMax
115k
ONT basecallers are [**performant only with GPU**][1]'s. [1]: https://hackmd.io/@Miles/B1U-cOMyu#GPUs-and-Guppy-base-calling
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
But it requires that there is a match between a part of the REF allele and a part of the ALT allele (https://github.com/samtools/htslib/blo…
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
// i and j are the position in the alt and ref string if ( a[i]!=END_OF_STRING && r[j]==END_OF-STRING ) { …
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
so looking quickly an indel is when this is not a symbolic allele (<BND>) and the length of REF and the current ALT are not the same.
Comment: bcftools stats: definition of indel type
by
WouterDeCoster
46k
Yes, but I cannot figure out in which cases the INDEL type is assigned: ``` if ( *a && !*r ) { if ( *a==']' || *a=='[' ) { …
Answer: MG RAST for Eukaryota
by
young_bioinformatician
▴ 170
Hi Tom, Yes, you can go with the predicted proteins for the annotation/downstream analysis.
Comment: bcftools stats: definition of indel type
by
Pierre Lindenbaum
145k
if the type hasn't been already defined, the type is set as an array of bytes using `OR` and this function: https://github.com/samtools/hts…
Comment: arrange samples in same order in rows and column in R
by
Kevin Blighe
81k
You probably just need: fit <- lmFit(t(mval), var) In your model, you are also attempting to adjust for a lot of covariates- is that…
Comment: arrange samples in same order in rows and column in R
by
Bioinfonext
▴ 380
Thank Basti, I already did this, could you please above posted full code? Many thanks,
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